Run revdep_details(, "abcrf")
for more info
checking whether package ‘abcrf’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/abcrf/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/abcrf/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/abcrf/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/abcrf/new/abcrf.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
data 2.6Mb
libs 5.3Mb
Run revdep_details(, "AlpsNMR")
for more info
checking running R code from vignettes ... ``` ‘Vig01-introduction-to-alpsnmr.Rmd’ using ‘UTF-8’... failed ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using ‘UTF-8’... OK ‘Vig02-handling-metadata-and-annotations.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: when running code in ‘Vig01-introduction-to-alpsnmr.Rmd’ ... NMRExperiment SubjectID TimePoint 1 10 Ana baseline
pca_outliers_rob <- nmr_pca_outliers_robust(dataset, + ncomp = 3)
When sourcing ‘Vig01-introduction-to-alpsnmr.R’: Error: x$k <= ncol(x$x) is not TRUE Execution halted ```
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b ad argument #1 to 'insert' (table expected, got nil) stack traceback: [C]: in function 'insert' .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk [C]: in function 'dofile' [string "\directlua "]:6: in main chunk. l.139 } ... LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’
SUMMARY: processing the following files failed: ‘Vig01-introduction-to-alpsnmr.Rmd’ ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ ‘Vig02-handling-metadata-and-annotations.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "AMARETTO")
for more info
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'get_firehoseData':
get_firehoseData
Code: function(TargetDirectory = "./", TCGA_acronym_uppercase =
"LUAD", dataType = "stddata", dataFileTag =
"mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
"tar.gz", gdacURL =
"https://gdac.broadinstitute.org/runs/", untarUngzip =
TRUE, printDisease_abbr = FALSE)
Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase =
"LUAD", dataType = "stddata", dataFileTag =
"mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
"tar.gz", gdacURL =
"http://gdac.broadinstitute.org/runs/", untarUngzip =
TRUE, printDisease_abbr = FALSE)
Mismatches in argument default values:
Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/"
checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 2.4Mb
checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Apache License (== 2.0) + file LICENSE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘knitr’
A package should be listed in only one of these fields.
'LinkingTo' field is unused: package has no 'src' directory
checking R code for possible problems ... NOTE
AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’
AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’
AMARETTO_HTMLreport: no visible binding for global variable
‘RegulatorIDs’
AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’
AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’
AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’
AMARETTO_HTMLreport: no visible binding for global variable ‘padj’
AMARETTO_HTMLreport: no visible binding for global variable
‘n_Overlapping’
...
GmtFromModules: no visible binding for global variable ‘GeneNames’
HyperGTestGeneEnrichment: no visible binding for global variable ‘i’
HyperGTestGeneEnrichment: no visible binding for global variable ‘j’
read_gct: no visible binding for global variable ‘Description’
Undefined global functions or variables:
Color Description GeneNames Genes Geneset Geneset_length ModuleNr
Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs
TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr
n_Overlapping overlap_perc p.value p_value padj q.value value
variable
checking data for non-ASCII characters ... NOTE
Note: found 152 marked UTF-8 strings
Run revdep_details(, "amplican")
for more info
checking running R code from vignettes ... ``` ‘amplicanFAQ.Rmd’ using ‘UTF-8’... OK ‘amplicanOverview.Rmd’ using ‘UTF-8’... OK ‘example_amplicon_report.Rmd’ using ‘UTF-8’... failed ‘example_barcode_report.Rmd’ using ‘UTF-8’... OK ‘example_group_report.Rmd’ using ‘UTF-8’... failed ‘example_guide_report.Rmd’ using ‘UTF-8’... failed ‘example_id_report.Rmd’ using ‘UTF-8’... failed ‘example_index.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: ...
src = sapply(config$ID, function(i) { + knitr::knit_expand(text = c("## {{i}} \n", "### Deletions \n", + paste("```{r del-{{i}}, echo ..." ... [TRUNCATED]
res = knitr::knit_child(text = src, quiet = TRUE)
When sourcing ‘example_id_report.R’: Error: character argument expected Execution halted ```
checking installed package size ... NOTE
installed size is 16.2Mb
sub-directories of 1Mb or more:
doc 13.7Mb
libs 1.6Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘CrispRVariants’
Run revdep_details(, "apollo")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/apollo/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/apollo/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/apollo/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/apollo/new/apollo.Rcheck/00install.out’ for details.
Run revdep_details(, "aroma.core")
for more info
Packages suggested but not available for checking:
'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Run revdep_details(, "aroma.light")
for more info
Found the following hidden files and directories:
inst/rsp/.rspPlugins
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Run revdep_details(, "autonomics")
for more info
checking examples ... ERROR ``` Running examples in ‘autonomics-Ex.R’ failed The error most likely occurred in:
Name: create_design
Title: Create design
Aliases: create_design
** Examples
file <- download_data('billing19.rnacounts.txt') ... Design: ~1 Intercept E00_R1 1
file <- download_data('atkin18.somascan.adat') Downloading atkin18.somascan.adat object <- read_somascan(file, plot=FALSE) Error in (1 + f_col):n_col : NA/NaN argument Calls: read_somascan -> .read_somascan Execution halted ```
checking tests ...
``
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 50 lines of output:
── Error ('test_3_read_somascan_atkin18.R:14:5'): read_somascan(file, subgroupvar = NULL) works ──
Error in
(1 + f_col):n_col`: NA/NaN argument
Backtrace:
▆
(1 + f_col):n_col
: NA/NaN argument
Backtrace:
▆[ FAIL 9 | WARN 0 | SKIP 0 | PASS 74 ] Error: Test failures Execution halted ```
checking running R code from vignettes ...
‘using_autonomics.Rmd’ using ‘UTF-8’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘using_autonomics.Rmd’
...
When sourcing ‘using_autonomics.R’:
Error: is_existing_file : Some or all of the files specified by file do not exist.
There was 1 failure:
Position
1 1
Value
1 /scratch/henrik/RtmpnCrIMk/datasets/GSE161731/GSE161731_counts.csv.gz
Cause
1 nonexistent
Execution halted
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘using_autonomics.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-2.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-3.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/autonomics/new/autonomics.Rcheck/vign_test/autonomics/vignettes/using_autonomics_files/figure-html/unnamed-chunk-2-4.png" but not available.
Quitting from lines at lines 63-76 [unnamed-chunk-3] (using_autonomics.Rmd) Error: processing vignette 'using_autonomics.Rmd' failed with diagnostics: ... 1 /scratch/henrik/Rtmp2GcwV8/datasets/GSE161731/GSE161731_counts.csv.gz Cause 1 nonexistent --- failed re-building ‘using_autonomics.Rmd’
SUMMARY: processing the following file failed: ‘using_autonomics.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "bahc")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "BASiCS")
for more info
Installation failed.
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/BASiCS/new/BASiCS.Rcheck/00install.out’ for details.
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
using C++11
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BASiCS.cpp -o BASiCS.o
In file included from /c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include/armadillo:514,
from /c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include/RcppArmadillo.h:29,
from libraries.h:11,
...
installing to /c4/home/henrik/repositories/matrixStats/revdep/checks/BASiCS/new/BASiCS.Rcheck/00LOCK-BASiCS/00new/BASiCS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error : in method for ‘Summary’ with signature ‘x="BASiCS_Chain"’: arguments (‘na.rm’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list
Error: unable to load R code in package ‘BASiCS’
Execution halted
ERROR: lazy loading failed for package ‘BASiCS’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/BASiCS/new/BASiCS.Rcheck/BASiCS’
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
using C++11
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c BASiCS.cpp -o BASiCS.o
In file included from /c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include/armadillo:514,
from /c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /c4/home/henrik/repositories/matrixStats/revdep/library/BASiCS/RcppArmadillo/include/RcppArmadillo.h:29,
from libraries.h:11,
...
installing to /c4/home/henrik/repositories/matrixStats/revdep/checks/BASiCS/old/BASiCS.Rcheck/00LOCK-BASiCS/00new/BASiCS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error : in method for ‘Summary’ with signature ‘x="BASiCS_Chain"’: arguments (‘na.rm’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list
Error: unable to load R code in package ‘BASiCS’
Execution halted
ERROR: lazy loading failed for package ‘BASiCS’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/BASiCS/old/BASiCS.Rcheck/BASiCS’
Run revdep_details(, "BatchQC")
for more info
checking R code for possible problems ... NOTE
gene_plot: no visible global function definition for ‘boxplot’
gene_plot: no visible binding for global variable ‘batch’
gls.series.C: no visible global function definition for ‘lm.fit’
sample_plot: no visible global function definition for ‘boxplot’
sample_plot: no visible binding for global variable ‘batch’
Undefined global functions or variables:
batch boxplot lm.fit
Consider adding
importFrom("graphics", "boxplot")
importFrom("stats", "lm.fit")
to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘BatchQCIntro.Rmd’ using rmarkdown --- finished re-building ‘BatchQCIntro.Rmd’
--- re-building ‘BatchQC_examples.Rmd’ using rmarkdown --- finished re-building ‘BatchQC_examples.Rmd’
--- re-building ‘BatchQC_usage_advanced.Rmd’ using rmarkdown ! LaTeX Error: File `iftex.sty' not found. ...
Error: processing vignette 'BatchQC_usage_advanced.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/BatchQC/new/BatchQC.Rcheck/vign_test/BatchQC/vignettes/BatchQC_usage_advanced.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See BatchQC_usage_advanced.log for more info. --- failed re-building ‘BatchQC_usage_advanced.Rmd’
SUMMARY: processing the following file failed: ‘BatchQC_usage_advanced.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "BayesfMRI")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE
installed size is 24.4Mb
sub-directories of 1Mb or more:
libs 24.1Mb
Run revdep_details(, "BayesianPlatformDesignTimeTrend")
for more info
checking installed package size ... NOTE
installed size is 133.2Mb
sub-directories of 1Mb or more:
data 1.3Mb
help 1.8Mb
libs 129.1Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "baystability")
for more info
Namespaces in Imports field not imported from:
‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
All declared Imports should be used.
Run revdep_details(, "bcf")
for more info
checking whether package ‘bcf’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/bcf/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/bcf/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/bcf/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/bcf/new/bcf.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
libs 8.4Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "bigPint")
for more info
checking examples ... ERROR ``` Running examples in ‘bigPint-Ex.R’ failed The error most likely occurred in:
Name: plotClusters
Title: Plot static parallel coordinate clusters
Aliases: plotClusters
** Examples
The first set of five examples use data and dataMetrics
... data(soybean_ir_sub) soybean_ir_sub[,-1] <- log(soybean_ir_sub[-1]+1) data(soybean_ir_sub_metrics) colList = c("#00A600FF", rainbow(5)[c(1,4,5)]) ret <- plotClusters(data=soybean_ir_sub, + dataMetrics = soybean_ir_sub_metrics, nC=4, colList = colList, + clusterAllData = FALSE, threshVal = 1e-7, saveFile = FALSE) Error in xtfrm.data.frame(x) : cannot xtfrm data frames Calls: plotClusters ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame Execution halted ```
checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Complete output: > BiocGenerics:::testPackage("bigPint") Error in xtfrm.data.frame(x) : cannot xtfrm data frames Error in xtfrm.data.frame(x) : cannot xtfrm data frames Error in xtfrm.data.frame(x) : cannot xtfrm data frames Error in xtfrm.data.frame(x) : cannot xtfrm data frames
... test_dataMetricsVolcano.R /c4/home/henrik/repositories/matrixStats/revdep/checks/bigPint/new/bigPint.Rcheck/bigPint/unitTests/test_dataMetricsVolcano.R
test_dataMetricsVolcanoApp.R
/c4/home/henrik/repositories/matrixStats/revdep/checks/bigPint/new/bigPint.Rcheck/bigPint/unitTests/test_dataMetricsVolcanoApp.R
Error in BiocGenerics:::testPackage("bigPint") : unit tests failed for package bigPint Execution halted ```
checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 2.0Mb
doc 2.3Mb
shiny-examples 3.0Mb
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘bioconductor.Rmd’ using rmarkdown Error: processing vignette 'bioconductor.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘bioconductor.Rmd’
--- re-building ‘manuscripts.Rmd’ using rmarkdown Error: processing vignette 'manuscripts.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ ... --- re-building ‘summarizedExperiment.Rmd’ using rmarkdown Error: processing vignette 'summarizedExperiment.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘summarizedExperiment.Rmd’
SUMMARY: processing the following files failed: ‘bioconductor.Rmd’ ‘manuscripts.Rmd’ ‘summarizedExperiment.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "bigstep")
for more info
checking running R code from vignettes ... ``` ‘bigstep.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘bigstep.Rmd’ ... Starting stepwise, 14 variables, crit = 180.8, MSE = 0.978. Done.
Xbig <- read.big.matrix("X.txt", sep = " ", header = TRUE, + backingfile = "X.bin", descriptorfile = "X.desc")
When sourcing ‘bigstep.R’: Error: The file X.txt could not be found Execution halted ```
Run revdep_details(, "bingat")
for more info
Package unavailable to check Rd xrefs: ‘genalg’
Run revdep_details(, "BioNERO")
for more info
installed size is 7.0Mb
sub-directories of 1Mb or more:
data 2.2Mb
doc 4.3Mb
Run revdep_details(, "biscuiteer")
for more info
checking whether package ‘biscuiteer’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/biscuiteer/new/biscuiteer.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 3.4Mb
checking package subdirectories ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’
See the note in ?`:::` about the use of this operator.
Run revdep_details(, "blackbox")
for more info
installed size is 15.1Mb
sub-directories of 1Mb or more:
libs 14.5Mb
Run revdep_details(, "BloodGen3Module")
for more info
checking whether package ‘BloodGen3Module’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘SummarizedExperiment::rowRanges’ by ‘matrixStats::rowRanges’ when loading ‘BloodGen3Module’
Warning: replacing previous import ‘SummarizedExperiment::start’ by ‘stats::start’ when loading ‘BloodGen3Module’
Warning: replacing previous import ‘SummarizedExperiment::end’ by ‘stats::end’ when loading ‘BloodGen3Module’
Warning: replacing previous import ‘matrixStats::rowRanges’ by ‘SummarizedExperiment::rowRanges’ when loading ‘BloodGen3Module’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/BloodGen3Module/new/BloodGen3Module.Rcheck/00install.out’ for details.
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
Run revdep_details(, "bnbc")
for more info
installed size is 8.3Mb
sub-directories of 1Mb or more:
cooler 2.9Mb
data 2.4Mb
libs 1.7Mb
Run revdep_details(, "bnclassify")
for more info
checking installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
libs 10.5Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘methods.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'methods.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/bnclassify/new/bnclassify.Rcheck/vign_test/bnclassify/vignettes/methods.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See methods.log for more info. --- failed re-building ‘methods.Rmd’ ...
Error: processing vignette 'usage.rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/bnclassify/new/bnclassify.Rcheck/vign_test/bnclassify/vignettes/usage.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See usage.log for more info. --- failed re-building ‘usage.rmd’
SUMMARY: processing the following files failed: ‘methods.Rmd’ ‘overview.Rmd’ ‘usage.rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "bnem")
for more info
Namespace in Imports field not imported from: ‘rmarkdown’
All declared Imports should be used.
Run revdep_details(, "brms")
for more info
R CMD check timed out
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE
installed size is 8.4Mb
sub-directories of 1Mb or more:
R 3.7Mb
doc 3.5Mb
Run revdep_details(, "BSgenome")
for more info
checking examples ... ERROR ``` Running examples in ‘BSgenome-Ex.R’ failed The error most likely occurred in:
Name: SNPlocs-class
Title: SNPlocs objects
Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs
ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs
OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method
providerVersion,SNPlocs-method releaseDate,SNPlocs-method releaseName
releaseName,SNPlocs-method referenceGenome
... seqlevelsStyle(my_cds) # UCSC [1] "UCSC" seqlevelsStyle(snps) # NCBI [1] "NCBI" seqlevelsStyle(my_cds) <- seqlevelsStyle(snps) Error in find_NCBI_assembly_ftp_dir(assembly_accession, assembly_name = assembly_name) : unable to find FTP dir for assembly GCF_000001405.40 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ Calls: seqlevelsStyle<- ... .form_assembly_report_url -> find_NCBI_assembly_ftp_dir Execution halted ```
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’
‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’
‘forgeMaskedBSgenomeDataPkg’
‘getBatchesByOverlapsFromOnDiskLongTable’
‘getBatchesBySeqnameFromOnDiskLongTable’
‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’
‘getRowsByIdFromOnDiskLongTable’
‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’
‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’
...
generic 'seqinfo' and siglist 'TwobitNamedSequences'
generic 'seqnames' and siglist 'OnDiskNamedSequences'
generic 'show' and siglist 'OnDiskLongTable'
generic 'show' and siglist 'OnDiskLongTable_old'
generic 'show' and siglist 'OnDiskNamedSequences'
generic 'spatialIndex' and siglist 'OnDiskLongTable'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking for portable file names ... NOTE ``` Found the following non-portable file path: BSgenome/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R
Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```
checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 5.5Mb
checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
inst/extdata/GentlemanLab/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION
Most likely ‘inst/CITATION’ should be used instead.
checking dependencies in R code ... NOTE
':::' calls which should be '::':
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’
‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’
See the note in ?`:::` about the use of this operator.
Run revdep_details(, "BSW")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "bulkAnalyseR")
for more info
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 3.4Mb
Run revdep_details(, "bumphunter")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach',
'iterators', 'parallel', 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
bootstraps
Run revdep_details(, "CARBayesST")
for more info
installed size is 11.3Mb
sub-directories of 1Mb or more:
R 1.0Mb
libs 9.2Mb
Run revdep_details(, "cardelino")
for more info
Package which this enhances but not available for checking: ‘doMC’
Run revdep_details(, "CATALYST")
for more info
installed size is 14.4Mb
sub-directories of 1Mb or more:
data 3.1Mb
doc 10.0Mb
Run revdep_details(, "causalOT")
for more info
installed size is 9.2Mb
sub-directories of 1Mb or more:
R 1.6Mb
libs 7.0Mb
Run revdep_details(, "ccImpute")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
libs 8.1Mb
Run revdep_details(, "celda")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘singleCellTK’
checking installed package size ... NOTE
installed size is 14.3Mb
sub-directories of 1Mb or more:
doc 3.2Mb
libs 9.7Mb
Run revdep_details(, "CelliD")
for more info
checking whether package ‘CelliD’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/CelliD/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/CelliD/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/CelliD/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
Warning: replacing previous import ‘data.table::shift’ by ‘tictoc::shift’ when loading ‘CelliD’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/CelliD/new/CelliD.Rcheck/00install.out’ for details.
checking examples ... WARNING ``` Found the following significant warnings:
Warning: 'as(, "dsTMatrix")' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
doc 3.1Mb
libs 3.4Mb
Run revdep_details(, "cellWise")
for more info
checking running R code from vignettes ... ``` ‘Correspondence_analysis_examples.Rmd’ using ‘UTF-8’... OK ‘DDC_examples.Rmd’ using ‘UTF-8’... OK ‘DI_examples.Rmd’ using ‘UTF-8’... OK ‘MacroPCA_examples.Rmd’ using ‘UTF-8’... OK ‘cellMCD_examples.Rmd’ using ‘UTF-8’... failed ‘cellwise_weights_examples.Rmd’ using ‘UTF-8’... OK ‘transfo_examples.Rmd’ using ‘UTF-8’... OK ‘wrap_examples.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: ...
At least one variable of X has more than 100*(1-alpha)% = 25% of marginal outliers. The percentages per variable are: X1 X2 X3 X4 Y 0.00 4.35 13.04 4.35 30.43
When sourcing ‘cellMCD_examples.R’: Error: Too many marginal outliers. Execution halted ```
checking whether package ‘cellWise’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/cellWise/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/cellWise/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/cellWise/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/cellWise/new/cellWise.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘GSE’
checking installed package size ... NOTE
installed size is 19.8Mb
sub-directories of 1Mb or more:
data 3.1Mb
doc 1.9Mb
libs 14.3Mb
Run revdep_details(, "CEMiTool")
for more info
checking installed package size ... NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
data 3.1Mb
doc 2.4Mb
extdata 2.8Mb
checking R code for possible problems ... NOTE
flip_vector: no visible global function definition for ‘setNames’
select_genes: no visible global function definition for ‘var’
get_hubs,CEMiTool : <anonymous>: no visible global function definition
for ‘head’
get_merged_mods,CEMiTool: no visible global function definition for
‘as.dist’
get_mods,CEMiTool: no visible global function definition for ‘as.dist’
get_phi,CEMiTool: no visible global function definition for ‘tail’
get_phi,CEMiTool: no visible global function definition for ‘head’
mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’
...
save_plots,CEMiTool: no visible global function definition for
‘dev.off’
Undefined global functions or variables:
..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist
head modules num_genes setNames tail var
Consider adding
importFrom("grDevices", "dev.off")
importFrom("stats", "as.dist", "dist", "setNames", "var")
importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Run revdep_details(, "ChAMP")
for more info
checking whether package ‘ChAMP’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores)
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ChAMP/new/ChAMP.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
checking Rd \usage sections ... WARNING ``` Duplicated \argument entries in documentation object 'champ.SVD': ‘Rplot’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db',
'IlluminaHumanMethylationEPICmanifest', 'DT', 'RPMM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
doc 3.6Mb
extdata 1.9Mb
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘rmarkdown’
A package should be listed in only one of these fields.
checking startup messages can be suppressed ... NOTE ``` No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'prettydoc'
All declared Imports should be used.
Package in Depends field not imported from: 'DT'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE
champ.DMR: possible error in dmrcate(myannotation, min.cpgs =
minProbes, lambda = lambda, C = C, mc.cores = cores): unused argument
(mc.cores = cores)
champ.ebGSEA : gseaWTfn: no visible global function definition for
'wilcox.test'
champ.ebGSEA: no visible global function definition for 'stopCluster'
champ.norm: no visible global function definition for 'stopCluster'
champ.process: no visible global function definition for 'champ.EpiMod'
Undefined global functions or variables:
champ.EpiMod stopCluster wilcox.test
Consider adding
importFrom("stats", "wilcox.test")
to your NAMESPACE file.
Run revdep_details(, "ChemoSpec2D")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘ChemoSpec2D.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'ChemoSpec2D.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/ChemoSpec2D/new/ChemoSpec2D.Rcheck/vign_test/ChemoSpec2D/vignettes/ChemoSpec2D.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See ChemoSpec2D.log for more info. --- failed re-building ‘ChemoSpec2D.Rmd’
SUMMARY: processing the following file failed: ‘ChemoSpec2D.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "ChIPpeakAnno")
for more info
checking examples ... ERROR ``` Running examples in ‘ChIPpeakAnno-Ex.R’ failed The error most likely occurred in:
Name: findEnhancers
Title: Find possible enhancers depend on DNA interaction data
Aliases: findEnhancers
Keywords: misc
** Examples
... Try to keep the seqname style consistent.
Try to keep the seqname style consistent.
data("myPeakList") seqlevelsStyle(myPeakList) <- seqlevelsStyle(annoData) <- seqlevelsStyle(DNAinteractiveData) Error in find_NCBI_assembly_ftp_dir(assembly_accession, assembly_name = assembly_name) : unable to find FTP dir for assembly GCF_000001405.25 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ Calls: seqlevelsStyle<- ... .form_assembly_report_url -> find_NCBI_assembly_ftp_dir Execution halted ```
checking running R code from vignettes ... ``` ‘ChIPpeakAnno.Rmd’ using ‘UTF-8’... OK ‘FAQs.Rmd’ using ‘UTF-8’... failed ‘pipeline.Rmd’ using ‘UTF-8’... failed ‘quickStart.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘FAQs.Rmd’ ...
knitr::opts_chunk$set(echo = TRUE, eval = FALSE, warning = FALSE, ... peak12338.NA peak12339.NA
seqinfo: 1 sequence from an unspecified genome; no seqlengths
pie1(table(anno$insideFeature))
When sourcing 'quickStart.R': Error: 'length.out' must be a finite number Execution halted ```
checking installed package size ... NOTE
installed size is 25.2Mb
sub-directories of 1Mb or more:
data 12.6Mb
doc 6.2Mb
extdata 5.2Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ensembldb’
All declared Imports should be used.
checking Rd files ... NOTE
checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown --- finished re-building ‘ChIPpeakAnno.Rmd’
--- re-building ‘FAQs.Rmd’ using rmarkdown --- finished re-building ‘FAQs.Rmd’
--- re-building ‘pipeline.Rmd’ using rmarkdown
Quitting from lines at lines 154-167 [workflow3] (pipeline.Rmd) ... Quitting from lines at lines 65-72 [annotate] (quickStart.Rmd) Error: processing vignette 'quickStart.Rmd' failed with diagnostics: 'length.out' must be a finite number --- failed re-building ‘quickStart.Rmd’
SUMMARY: processing the following files failed: ‘pipeline.Rmd’ ‘quickStart.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "chromswitch")
for more info
Found the following significant warnings:
Warning: Package 'chromswitch' is deprecated and will be removed from
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/chromswitch/new/chromswitch.Rcheck/00install.out’ for details.
Run revdep_details(, "cifti")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "cliqueMS")
for more info
Installation failed.
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/cliqueMS/new/cliqueMS.Rcheck/00install.out’ for details.
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
using C++11
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c findAnnotationR.cpp -o findAnnotationR.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c findCliquesR.cpp -o findCliquesR.o
In file included from /c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include/armadillo:514,
from /c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘cliqueMS’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/cliqueMS/new/cliqueMS.Rcheck/cliqueMS’
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
using C++11
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c findAnnotationR.cpp -o findAnnotationR.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/Rcpp/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/BH/include' -I'/c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c findCliquesR.cpp -o findCliquesR.o
In file included from /c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include/armadillo:514,
from /c4/home/henrik/repositories/matrixStats/revdep/library/cliqueMS/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘cliqueMS’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/cliqueMS/old/cliqueMS.Rcheck/cliqueMS’
Run revdep_details(, "clusterExperiment")
for more info
checking running R code from vignettes ... ``` ‘clusterExperimentTutorial.Rmd’ using ‘UTF-8’... failed ‘largeDataSets.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: when running code in ‘clusterExperimentTutorial.Rmd’ ...
ce <- makeConsensus(ce, whichCluster = wh, proportion = 0.7, + minSize = 3, clusterLabel = "makeConsensus,nVAR")
plotCoClustering(ce)
When sourcing ‘clusterExperimentTutorial.R’: Error: invalid graphics state Execution halted ```
checking contents of ‘data’ directory ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
Search path was changed
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 18.0Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 3.6Mb
doc 10.4Mb
libs 2.2Mb
checking foreign function calls ... NOTE
Foreign function calls to a different package:
.C(ape::node_depth, ...)
.C(ape::node_depth_edgelength, ...)
.C(ape::node_height, ...)
.C(ape::node_height_clado, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘scRNAseq’, ‘ConsensusClusterPlus’
Run revdep_details(, "clustifyr")
for more info
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 2.1Mb
doc 1.5Mb
help 1.1Mb
checking R code for possible problems ... NOTE
gmt_to_list: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
Run revdep_details(, "cmapR")
for more info
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.dockerignore
docs/build/html/.buildinfo
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 2.3Mb
extdata 2.1Mb
checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocManager’
'library' or 'require' call not declared from: ‘BiocManager’
Run revdep_details(, "cna")
for more info
checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
libs 7.8Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘cna.Rnw’ using Sweave
Registered S3 method overwritten by 'cna':
method from
some.data.frame car
Error: processing vignette 'cna.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cna.tex' failed.
LaTeX errors:
! LaTeX Error: File
nicefrac.sty' not found.
... l.12 \usepackage {float}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'cna.Rnw'
SUMMARY: processing the following file failed: 'cna.Rnw'
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "CNVScope")
for more info
checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
doc 3.2Mb
extdata 1.7Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'Hmisc'
All declared Imports should be used.
Run revdep_details(, "coin")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘Implementation.Rnw’ using Sweave Loading required package: survival Loading required package: grid --- finished re-building ‘Implementation.Rnw’
--- re-building ‘LegoCondInf.Rnw’ using Sweave Loading required package: coin Loading required package: survival Error: processing vignette 'LegoCondInf.Rnw' failed with diagnostics: ... Warning in .local(object, ...) : p-values may be incorrect due to violation of the subset pivotality condition --- finished re-building ‘coin.Rnw’
SUMMARY: processing the following file failed: ‘LegoCondInf.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "cola")
for more info
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 3.2Mb
extdata 1.0Mb
libs 2.3Mb
Run revdep_details(, "compcodeR")
for more info
Packages which this enhances but not available for checking:
'rpanel', 'DSS'
Run revdep_details(, "condiments")
for more info
.condition_sling: no visible binding for global variable ‘.’
.condition_sling : <anonymous>: no visible binding for global variable
‘.’
.distinct_inputs: no visible binding for global variable ‘Samples’
.distinct_inputs: no visible binding for global variable ‘.’
.fateSelectionTest: no visible binding for global variable ‘pair’
.fateSelectionTest: no visible binding for global variable ‘statistic’
.fateSelectionTest: no visible binding for global variable ‘p.value’
.multiple_samples: no visible binding for global variable ‘p.value’
.progressionTest: no visible binding for global variable ‘lineage’
...
.progressionTest: no visible binding for global variable ‘statistic’
.progressionTest: no visible binding for global variable ‘p.value’
.topologyTest_multipleSamples: no visible binding for global variable
‘p.value’
fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding
for global variable ‘condition’
progressionTest_multipleSamples,SlingshotDataSet: no visible binding
for global variable ‘condition’
Undefined global functions or variables:
. Samples condition lineage p.value pair statistic
Run revdep_details(, "conquer")
for more info
checking whether package ‘conquer’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/conquer/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/conquer/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/conquer/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/conquer/new/conquer.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 23.3Mb
sub-directories of 1Mb or more:
libs 23.1Mb
Run revdep_details(, "cophescan")
for more info
checking whether package ‘cophescan’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/cophescan/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/cophescan/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/cophescan/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/cophescan/new/cophescan.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
data 3.5Mb
libs 3.1Mb
Run revdep_details(, "corrcoverage")
for more info
checking whether package ‘corrcoverage’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/corrcoverage/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/corrcoverage/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/corrcoverage/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/corrcoverage/new/corrcoverage.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
extdata 3.8Mb
libs 1.4Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘data.table’
All declared Imports should be used.
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "crlmm")
for more info
checking Rd files ... WARNING
checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label
checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label
checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label
checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) snprma.Rd:38: Escaped LaTeX specials: \_ \_
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 2.7Mb
checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
checking startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘splines’
All declared Imports should be used.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
calculateRBafCNSet : processByChromosome: no visible global function
definition for ‘position’
genotypeInf: no visible binding for global variable ‘anno’
krlmm: no visible binding for global variable ‘VGLMparameters’
Undefined global functions or variables:
VGLMparameters anno defineTestSuite position printTextProtocol
runTestSuite
Run revdep_details(, "crossmeta")
for more info
checking examples ... ERROR ``` Running examples in ‘crossmeta-Ex.R’ failed The error most likely occurred in:
Name: es_meta
Title: Effect size combination meta analysis.
Aliases: es_meta
** Examples
... data_dir <- system.file("extdata", package = "lydata")
gather GSE names
gse_names <- c("GSE9601", "GSE15069", "GSE50841", "GSE34817", "GSE29689")
load previous analysis
anals <- load_diff(gse_names, data_dir) Error in readRDS(path) : unknown input format Calls: load_diff -> readRDS Execution halted ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RCurl’ ‘XML’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘GeneMeta’
Run revdep_details(, "cSEM")
for more info
Namespace in Imports field not imported from: ‘Rdpack’
All declared Imports should be used.
Run revdep_details(, "cytomapper")
for more info
checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
R 1.3Mb
doc 5.0Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘CATALYST’
Run revdep_details(, "DCATS")
for more info
checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
checking R code for possible problems ... NOTE
svm_simMat: no visible binding for global variable ‘clusterRes’
Undefined global functions or variables:
clusterRes
Run revdep_details(, "DCLEAR")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/DCLEAR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/DCLEAR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/DCLEAR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DCLEAR/new/DCLEAR.Rcheck/00install.out’ for details.
Run revdep_details(, "ddtlcm")
for more info
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 3.9Mb
Run revdep_details(, "decompr")
for more info
Package suggested but not available for checking: ‘gvc’
Run revdep_details(, "DeepBlueR")
for more info
Installation failed.
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeepBlueR/new/DeepBlueR.Rcheck/00install.out’ for details.
* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
status
"502"
Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) :
Problems
Error: unable to load R code in package ‘DeepBlueR’
Execution halted
ERROR: lazy loading failed for package ‘DeepBlueR’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeepBlueR/new/DeepBlueR.Rcheck/DeepBlueR’
* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
status
"502"
Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) :
Problems
Error: unable to load R code in package ‘DeepBlueR’
Execution halted
ERROR: lazy loading failed for package ‘DeepBlueR’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeepBlueR/old/DeepBlueR.Rcheck/DeepBlueR’
Run revdep_details(, "DelayedMatrixStats")
for more info
checking running R code from vignettes ... ``` ‘DelayedMatrixStatsOverview.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘DelayedMatrixStatsOverview.Rmd’ ... 149.601 4.605 154.345
head(row_sds) [1] 9.196538 6.580673 7.633720 5.974507 8.274247 10.438290
matrixStats::rowSds(x)
When sourcing ‘DelayedMatrixStatsOverview.R’: Error: Argument 'x' must be a matrix or a vector. Execution halted ```
checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: ‘DelayedArray:::.reduce_array_dimensions’
Unexported objects imported by ':::' calls:
‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::BLOCK_colVars’
‘DelayedArray:::BLOCK_rowVars’ ‘DelayedArray:::RleArraySeed’
‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::set_dim’
‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’
‘DelayedArray:::to_linear_index’
See the note in ?`:::` about the use of this operator.
Run revdep_details(, "DELocal")
for more info
installed size is 9.3Mb
sub-directories of 1Mb or more:
extdata 8.5Mb
Run revdep_details(, "DeMixT")
for more info
checking whether package ‘DeMixT’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeMixT/new/DeMixT.Rcheck/00install.out’ for details.
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'detect_suspicious_sample_by_hierarchical_clustering_2comp' ‘labels’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth',
'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 1.9Mb
libs 3.7Mb
checking R code for possible problems ... NOTE
DeMixT_GS: no visible global function definition for ‘qchisq’
DeMixT_preprocessing: no visible global function definition for
‘quantile_normalization’
detect_suspicious_sample_by_hierarchical_clustering_2comp :
<anonymous>: no visible global function definition for ‘wilcox.test’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘prcomp’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘dist’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
...
Undefined global functions or variables:
DataFrame SimpleList abline as.dendrogram dist hclust legend median
par points prcomp qchisq quantile_normalization rainbow segments
wilcox.test
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "legend", "par", "points", "segments")
importFrom("stats", "as.dendrogram", "dist", "hclust", "median",
"prcomp", "qchisq", "wilcox.test")
to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘calibrate’
Run revdep_details(, "DepecheR")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking compiled code ... NOTE ``` File ‘DepecheR/libs/DepecheR.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘Clusterer.o’ Found ‘srand’, possibly from ‘srand’ (C) Objects: ‘Clusterer.o’, ‘InterfaceUtils.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "DEqMS")
for more info
checking examples ... ERROR ``` Running examples in ‘DEqMS-Ex.R’ failed The error most likely occurred in:
Name: Residualplot
Title: plot the residuals against the number of quantified
peptides/PSMs.
Aliases: Residualplot
** Examples
... eh = ExperimentHub(localHub=TRUE) Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use query(eh, "DEqMS") ExperimentHub with 0 records
dat.psm = eh[["EH1663"]] Error: File not previously downloaded. Run with 'localHub=FALSE' Execution halted ```
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘matrixStats’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Run revdep_details(, "DESeq2")
for more info
checking whether package ‘DESeq2’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/DESeq2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/DESeq2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/DESeq2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DESeq2/new/DESeq2.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
doc 2.4Mb
libs 4.2Mb
Run revdep_details(, "detrendr")
for more info
checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
libs 9.2Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "DHS.rates")
for more info
Namespace in Imports field not imported from: ‘rlang’
All declared Imports should be used.
Run revdep_details(, "diffUTR")
for more info
checking R code for possible problems ... NOTE
deuBinPlot: no visible binding for global variable 'x_start'
deuBinPlot: no visible binding for global variable 'x_end'
deuBinPlot: no visible binding for global variable 'y_start'
deuBinPlot: no visible binding for global variable 'y_end'
plotTopGenes: no visible binding for global variable 'sizeScore'
plotTopGenes: no visible binding for global variable 'q.value'
plotTopGenes: no visible binding for global variable 'density.ratio'
plotTopGenes: no visible binding for global variable 'geneMeanDensity'
plotTopGenes: no visible binding for global variable 'w.abs.coef'
plotTopGenes: no visible binding for global variable 'tmp'
plotTopGenes: no visible binding for global variable 'name'
Undefined global functions or variables:
density.ratio geneMeanDensity name q.value sizeScore tmp w.abs.coef
x_end x_start y_end y_start
checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘ggbio’
Run revdep_details(, "Dino")
for more info
checkCounts: no visible global function definition for ‘as’
Undefined global functions or variables:
as
Consider adding
importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Run revdep_details(, "disbayes")
for more info
checking installed package size ... NOTE
installed size is 124.6Mb
sub-directories of 1Mb or more:
libs 123.8Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘disbayes.Rmd’ using rmarkdown
Quitting from lines at lines 254-259 [unnamed-chunk-6] (disbayes.Rmd) Error: processing vignette 'disbayes.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘disbayes.Rmd’
SUMMARY: processing the following file failed: ‘disbayes.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "DiscoRhythm")
for more info
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘data.table’
All declared Imports should be used.
checking R code for possible problems ... NOTE
discoApp: no visible binding for global variable ‘.discorhythm_ncores’
discoApp: no visible binding for global variable ‘.discorhythm_local’
discoBatch: no visible binding for global variable ‘discoODAres’
Undefined global functions or variables:
.discorhythm_local .discorhythm_ncores discoODAres
checking Rd files ... NOTE
checkRd: (-1) discoParseMeta.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) discoParseMeta.Rd:29: Escaped LaTeX specials: \_
Run revdep_details(, "dmrseq")
for more info
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 4.8Mb
doc 1.3Mb
Run revdep_details(, "Doscheda")
for more info
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 2.1Mb
doc 1.6Mb
shiny-examples 1.9Mb
Run revdep_details(, "DSWE")
for more info
checking whether package ‘DSWE’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/DSWE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/DSWE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/DSWE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DSWE/new/DSWE.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 10.5Mb
sub-directories of 1Mb or more:
data 2.8Mb
libs 7.4Mb
Run revdep_details(, "dwp")
for more info
Namespaces in Imports field not imported from:
‘GenEst’ ‘expint’ ‘numDeriv’
All declared Imports should be used.
Run revdep_details(, "eaf")
for more info
GNU make is a SystemRequirements.
Run revdep_details(, "easier")
for more info
checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘reannotate_genes’
checking R code for possible problems ... NOTE
compute_TF_activity: no visible binding for global variable ‘condition’
compute_TF_activity: no visible binding for global variable ‘score’
Undefined global functions or variables:
condition score
Run revdep_details(, "ecospat")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘vignette_ecospat_package.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'vignette_ecospat_package.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/ecospat/new/ecospat.Rcheck/vign_test/ecospat/vignettes/vignette_ecospat_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette_ecospat_package.log for more info. --- failed re-building ‘vignette_ecospat_package.Rmd’
SUMMARY: processing the following file failed: ‘vignette_ecospat_package.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "EMDomics")
for more info
checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre]
Daniel Schmolze <emd@schmolze.com> [aut, cre]
checking R code for possible problems ... NOTE
.cvm_pairwise_q: no visible global function definition for ‘combn’
.cvm_pairwise_q : <anonymous>: no visible global function definition
for ‘median’
.emd_gene_pairwise: no visible global function definition for ‘hist’
.emd_pairwise_q: no visible global function definition for ‘combn’
.emd_pairwise_q : <anonymous>: no visible global function definition
for ‘median’
.ks_pairwise_table: no visible global function definition for ‘ks.test’
calculate_cvm: no visible global function definition for ‘combn’
calculate_cvm : <anonymous>: no visible global function definition for
...
‘median’
calculate_ks_gene: no visible global function definition for ‘combn’
calculate_ks_gene: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
combn hist ks.test median p.adjust
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "ks.test", "median", "p.adjust")
importFrom("utils", "combn")
to your NAMESPACE file.
Run revdep_details(, "ENmix")
for more info
installed size is 21.0Mb
sub-directories of 1Mb or more:
doc 2.3Mb
Run revdep_details(, "EnrichedHeatmap")
for more info
installed size is 16.3Mb
sub-directories of 1Mb or more:
doc 13.3Mb
extdata 1.6Mb
libs 1.2Mb
Run revdep_details(, "EpiDISH")
for more info
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Run revdep_details(, "epimutacions")
for more info
checking running R code from vignettes ... ``` ‘epimutacions.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘epimutacions.Rmd’ ... > reference_panel <- eh[["EH6691"]] see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation loading from cache
When sourcing 'epimutacions.R': Error: failed to load resource name: EH6691 title: Reference panel reason: error in evaluating the argument 'x' in selecting a method for function 'get': error reading from connection Execution halted ```
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘CompQuadForm’, ‘car’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘epimutacions.Rmd’ using rmarkdown
Quitting from lines at lines 610-611 [annot] (epimutacions.Rmd) Error: processing vignette 'epimutacions.Rmd' failed with diagnostics: Multiple cache results found. Please clear your cache by running biomartCacheClear() --- failed re-building ‘epimutacions.Rmd’
SUMMARY: processing the following file failed: ‘epimutacions.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "epistasisGA")
for more info
checking whether package ‘epistasisGA’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/epistasisGA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/epistasisGA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/epistasisGA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/epistasisGA/new/epistasisGA.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 13.7Mb
sub-directories of 1Mb or more:
doc 4.0Mb
libs 9.3Mb
Run revdep_details(, "eseis")
for more info
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
Run revdep_details(, "evaluomeR")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc',
'randomForest', 'flexmix'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘kableExtra’
All declared Imports should be used.
Packages in Depends field not imported from:
‘flexmix’ ‘randomForest’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Run revdep_details(, "EventPointer")
for more info
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’ ‘SGSeq:::edges’
‘SGSeq:::exonGraph’ ‘SGSeq:::feature2name’ ‘SGSeq:::matchSGFeatures’
‘SGSeq:::nodes’ ‘SGSeq:::propagateAnnotation’
‘SGSeq:::splitCharacterList’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
EventDetection_transcriptome: no visible binding for global variable
‘jj’
SF_Prediction: no visible binding for global variable ‘valueRanking’
SF_Prediction: no visible binding for global variable ‘PSI_table’
annotate2: no visible global function definition for
‘addDummySpliceSites’
annotate2: no visible global function definition for ‘annotatePaths’
annotateFeatures2: no visible global function definition for
‘matchTxFeatures’
callGRseq_parallel: no visible global function definition for
...
‘stopCluster’
fitgl: no visible binding for global variable ‘hist’
myphyper: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
PSI_table addDummySpliceSites annotatePaths dhyper hist i ii jj
makeCluster matchTxFeatures stopCluster valueRanking
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "dhyper")
to your NAMESPACE file.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'InternalFunctions': ‘sort.exons’
The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "ExCluster")
for more info
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Run revdep_details(, "ExpHunterSuite")
for more info
checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
example 1.9Mb
extData 3.9Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘EnhancedVolcano’ ‘biomaRt’ ‘ggupset’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘clusterProfiler:::enricher_internal’ ‘enrichplot:::fortify.internal’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ``` Found the following possibly unsafe calls: File ‘ExpHunterSuite/R/write_report.R’: assignInNamespace("clean_tmpfiles", clean_tmpfiles_mod, ns = "rmarkdown") assignInNamespace("clean_tmpfiles", clean_tmpfiles_mod, ns = "rmarkdown")
enrich_density: no visible binding for global variable ‘attribute’ enrich_density: no visible binding for global variable ‘Description’ enrich_density: no visible binding for global variable ‘p.adjust’ get_kegg_db_path: no visible binding for global variable ‘root_path’ get_miRNA_ct: no visible binding for global variable ‘sig_pairs’ ... get_sig_genes: no visible binding for global variable ‘genes_tag’ main_degenes_Hunter: no visible binding for global variable ‘Row.names’ write_global_cormit: no visible global function definition for ‘aggregate’ Undefined global functions or variables: Description Row.names aggregate attribute genes_tag p.adjust root_path sig_pairs Consider adding importFrom("stats", "aggregate", "p.adjust") to your NAMESPACE file. ```
Run revdep_details(, "ExpressionNormalizationWorkflow")
for more info
checking whether package ‘ExpressionNormalizationWorkflow’ can be installed ... WARNING
Found the following significant warnings:
Warning: ExpressionNormalizationWorkflow-package.Rd:29: All text must be in a section
Warning: ExpressionNormalizationWorkflow-package.Rd:30: All text must be in a section
Warning: replacing previous import ‘Biobase::rowMedians’ by ‘matrixStats::rowMedians’ when loading ‘ExpressionNormalizationWorkflow’
Warning: replacing previous import ‘Biobase::anyMissing’ by ‘matrixStats::anyMissing’ when loading ‘ExpressionNormalizationWorkflow’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ExpressionNormalizationWorkflow/new/ExpressionNormalizationWorkflow.Rcheck/00install.out’ for details.
checking Rd files ... WARNING
prepare_Rd: ExpressionNormalizationWorkflow-package.Rd:29: All text must be in a section
prepare_Rd: ExpressionNormalizationWorkflow-package.Rd:30: All text must be in a section
checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
doc 2.5Mb
extdata 4.7Mb
checking R code for possible problems ... NOTE
expSetobj: no visible global function definition for ‘new’
pvcAnaly: no visible global function definition for ‘barplot’
pvcAnaly: no visible global function definition for ‘axis’
pvcAnaly: no visible global function definition for ‘text’
pvcaBatchAssess: no visible global function definition for ‘cor’
pvcaBatchAssess: no visible binding for global variable ‘na.omit’
pvcaBatchAssess: no visible global function definition for ‘sigma’
snmAnaly: no visible global function definition for ‘model.matrix’
snmAnaly: no visible global function definition for ‘write.table’
surVarAnaly: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
axis barplot cor model.matrix na.omit new sigma text write.table
Consider adding
importFrom("graphics", "axis", "barplot", "text")
importFrom("methods", "new")
importFrom("stats", "cor", "model.matrix", "na.omit", "sigma")
importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking Rd cross-references ... NOTE
Unknown package ‘<pkg>’ in Rd xrefs
checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocManager’
Run revdep_details(, "extraChIPs")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside',
'SummarizedExperiment', 'tibble'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Run revdep_details(, "fastcpd")
for more info
R CMD check timed out
checking whether package ‘fastcpd’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/fastcpd/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/fastcpd/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/fastcpd/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/fastcpd/new/fastcpd.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 24.5Mb
sub-directories of 1Mb or more:
doc 4.2Mb
help 1.8Mb
libs 17.4Mb
Run revdep_details(, "FastPCS")
for more info
installed size is 14.8Mb
sub-directories of 1Mb or more:
libs 14.7Mb
Run revdep_details(, "FastRCS")
for more info
installed size is 20.5Mb
sub-directories of 1Mb or more:
libs 20.4Mb
Run revdep_details(, "fastverse")
for more info
Namespaces in Imports field not imported from:
‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
All declared Imports should be used.
Run revdep_details(, "FDb.FANTOM4.promoters.hg19")
for more info
checking package subdirectories ... WARNING
Found the following non-empty subdirectories of ‘inst’ also used by R:
inst/build
It is recommended not to interfere with package subdirectories used by
R.
checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicFeatures’
A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘BSgenome.Hsapiens.UCSC.hg19’ ‘matrixStats’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Biostrings’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘matrixStats:::rowProds’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
oecg: no visible global function definition for ‘is’
oecg: no visible global function definition for ‘seqlengths’
oecg: no visible binding for global variable ‘Hsapiens’
oecg: no visible global function definition for ‘seqlevels’
oecg: no visible global function definition for ‘seqnames’
oecg: no visible global function definition for ‘resize’
oecg: no visible global function definition for ‘start’
oecg: no visible global function definition for ‘start<-’
oecg: no visible global function definition for ‘end’
oecg: no visible global function definition for ‘end<-’
...
oecg: no visible global function definition for ‘letterFrequency’
oecg: no visible global function definition for ‘dinucleotideFrequency’
Undefined global functions or variables:
Hsapiens dinucleotideFrequency end end<- getSeq is letterFrequency
resize seqlengths seqlevels seqnames start start<- width
Consider adding
importFrom("methods", "is")
importFrom("stats", "end", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Run revdep_details(, "FEAST")
for more info
checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 3.9Mb
doc 1.3Mb
checking R code for possible problems ... NOTE
FEAST: multiple local function definitions for ‘bp_fun’ with different
formal arguments
SC3_Clust: no visible global function definition for ‘metadata’
Visual_Rslt: no visible global function definition for ‘ggbarplot’
Visual_Rslt: no visible global function definition for ‘theme’
Visual_Rslt: no visible global function definition for ‘element_text’
Visual_Rslt: no visible global function definition for ‘ggline’
Visual_Rslt: no visible global function definition for ‘get_palette’
Visual_Rslt: no visible global function definition for
‘scale_y_continuous’
Visual_Rslt: no visible global function definition for ‘guides’
Visual_Rslt: no visible global function definition for ‘guide_legend’
Visual_Rslt: no visible global function definition for ‘ggarrange’
aricode_NMI : entropy: no visible global function definition for
‘sortPairs’
Undefined global functions or variables:
element_text get_palette ggarrange ggbarplot ggline guide_legend
guides metadata scale_y_continuous sortPairs theme
Run revdep_details(, "fipp")
for more info
checking whether package ‘fipp’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/fipp/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/fipp/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/fipp/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/fipp/new/fipp.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "fishpond")
for more info
checking running R code from vignettes ... ``` ‘allelic.Rmd’ using ‘UTF-8’... failed ‘swish.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: when running code in ‘allelic.Rmd’ ...
gene <- rowRanges(y)$gene_id[1]
plotAllelicGene(y, gene, edb)
When sourcing 'allelic.R': Error: unable to find FTP dir for assembly GCF_000001405.40 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ Execution halted ```
checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 5.0Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'samr:::localfdr' 'samr:::predictlocalfdr' 'samr:::qvalue.func'
'samr:::samr.compute.delta.table.seq'
See the note in ?`:::` about the use of this operator.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘allelic.Rmd’ using rmarkdown
Quitting from lines at lines 306-308 [unnamed-chunk-12] (allelic.Rmd) Error: processing vignette 'allelic.Rmd' failed with diagnostics: unable to find FTP dir for assembly GCF_000001405.40 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ --- failed re-building ‘allelic.Rmd’
--- re-building ‘swish.Rmd’ using rmarkdown --- finished re-building ‘swish.Rmd’
SUMMARY: processing the following file failed: ‘allelic.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "flowCore")
for more info
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘multiRangeGate’
Undocumented S4 classes:
‘multiRangeGate’
Undocumented S4 methods:
generic '%in%' and siglist 'flowFrame,multiRangeGate'
generic 'show' and siglist 'multiRangeGate'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking compiled code ... WARNING ``` File ‘flowCore/libs/flowCore.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Object: ‘fcsTextParse.o’ Found ‘sprintf’, possibly from ‘sprintf’ (C) Object: ‘Logicle.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 17.9Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 5.4Mb
extdata 1.1Mb
libs 9.0Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
checking Rd files ... NOTE
checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^
checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^
checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘HowTo-flowCore.Rnw’ using knitr
Error: processing vignette 'HowTo-flowCore.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'HowTo-flowCore.tex' failed.
LaTeX errors:
! LaTeX Error: File
comment.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.65 \usepackage {graphicx}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘HowTo-flowCore.Rnw’
SUMMARY: processing the following file failed: ‘HowTo-flowCore.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "flowGraph")
for more info
checking R code for possible problems ... NOTE
get_child: no visible binding for global variable ‘no_cores’
get_paren: no visible binding for global variable ‘no_cores’
ms_psig: no visible binding for global variable ‘meta’
Undefined global functions or variables:
meta no_cores
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘doParallel’
Run revdep_details(, "flowWorkspace")
for more info
checking Rd cross-references ... WARNING ``` Package unavailable to check Rd xrefs: ‘flowStats’ Missing link or links in documentation object 'gs_plot_pop_count_cv.Rd': ‘barchart’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘gs_clone’ ‘gs_copy_tree_only’
Undocumented S4 methods:
generic 'dimnames' and siglist 'cytoframe'
generic 'rownames' and siglist 'cytoframe'
generic 'rownames<-' and siglist 'cytoframe'
generic 'show' and siglist 'cytoframe'
generic 'transform' and siglist 'cytoframe'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object 'GatingSet-methods': ‘...’
Undocumented arguments in documentation object 'convert' ‘backend’
Undocumented arguments in documentation object 'cs_get_uri' ‘x’
Undocumented arguments in documentation object 'gh_apply_to_new_fcs' ... ‘backend’ ‘backend_dir’
Undocumented arguments in documentation object 'save_gs' ‘cdf’ ‘backend_readonly’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
-Wno-pedantic -w -Wfatal-errors
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
checking installed package size ... NOTE
installed size is 73.2Mb
sub-directories of 1Mb or more:
doc 3.5Mb
libs 68.4Mb
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
AGPL-3.0-only
Standardizable: FALSE
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RBGL’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘DelayedArray:::simplify_NULL_dimnames’ ‘flowCore:::.estimateLogicle’
‘flowCore:::.spillover_pattern’ ‘flowCore:::checkClass’
‘flowCore:::guid’ ‘flowCore:::logicle_transform’
‘flowCore:::parse_pd_for_read_fs’ ‘flowCore:::txt2spillmatrix’
‘flowCore:::updateTransformKeywords’
‘flowCore:::validFilterResultList’ ‘graph:::.makeEdgeKeys’
‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’
See the note in ?`:::` about the use of this operator.
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
checking compiled code ... NOTE ``` File ‘flowWorkspace/libs/flowWorkspace.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Objects: ‘R_GatingSet.o’, ‘cytoframeAPI.o’, ‘cytosetAPI.o’ Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘R_GatingSet.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "footBayes")
for more info
Namespace in Imports field not imported from: ‘tidyverse’
All declared Imports should be used.
Run revdep_details(, "FRASER")
for more info
checking whether package ‘FRASER’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/FRASER/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/FRASER/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/FRASER/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/FRASER/new/FRASER.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
R 1.3Mb
doc 1.6Mb
libs 6.0Mb
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
See the note in ?`:::` about the use of this operator.
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘FRASER.Rnw’ using knitr
Error: processing vignette 'FRASER.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'FRASER.tex' failed.
LaTeX errors:
! LaTeX Error: File
nowidow.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘FRASER.Rnw’
SUMMARY: processing the following file failed: ‘FRASER.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "funtooNorm")
for more info
checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object 'show,SampleSet-method': ‘...’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘MyEndnoteLibrary.bib’ ‘funtooNorm.Rmd’ ‘funtooNorm.pdf’
‘validationcurvesPCRlow.jpg’
Files named as vignettes but with no recognized vignette engine:
‘vignettes/funtooNorm.Rmd’
(Is a VignetteBuilder field missing?)
Run revdep_details(, "gap")
for more info
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘shiny’
checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
doc 7.9Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘car’
Run revdep_details(, "geneticae")
for more info
Namespaces in Imports field not imported from:
‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
‘reshape2’
All declared Imports should be used.
Run revdep_details(, "GeneTonic")
for more info
checking installed package size ... NOTE
installed size is 17.4Mb
sub-directories of 1Mb or more:
data 1.2Mb
doc 14.0Mb
extdata 1.4Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘pcaExplorer’
Run revdep_details(, "genomation")
for more info
checking whether package ‘genomation’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/genomation/new/genomation.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
doc 3.5Mb
extdata 1.2Mb
libs 2.0Mb
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
definition for ‘:=’
Undefined global functions or variables:
:= id
Run revdep_details(, "geocmeans")
for more info
checking whether package ‘geocmeans’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/geocmeans/new/geocmeans.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 13.5Mb
sub-directories of 1Mb or more:
extdata 3.0Mb
libs 8.2Mb
Run revdep_details(, "geva")
for more info
checking running R code from vignettes ... ``` ‘geva.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘geva.Rmd’ ...
When sourcing ‘geva.R’: Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in '/scratch/henrik/RtmpDq40Lr/file428d26607f3/vignettes'. ℹ Are you in your project directory and does your project have a 'DESCRIPTION' file? Execution halted ```
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘geva.Rmd’ using rmarkdown Warning in Sys.setlocale("LC_TIME", "English_United States") : OS reports request to set locale to "English_United States" cannot be honored The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-summary-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-quantiles-1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-quantiles-2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-cluster-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-cluster-grouped-1.png" but not available. ...
Error: processing vignette 'geva.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See geva.log for more info. --- failed re-building ‘geva.Rmd’
SUMMARY: processing the following file failed: ‘geva.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "ggdmc")
for more info
checking whether package ‘ggdmc’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/ggdmc/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/ggdmc/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/ggdmc/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ggdmc/new/ggdmc.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 9.0Mb
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "GGPA")
for more info
checking whether package ‘GGPA’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/GGPA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/GGPA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/GGPA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/GGPA/new/GGPA.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
doc 1.6Mb
libs 4.7Mb
checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘network’ ‘scales’ ‘sna’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking compiled code ... NOTE ``` File ‘GGPA/libs/GGPA.so’: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘3_Param.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "GJRM")
for more info
Package which this enhances but not available for checking: ‘sp’
Run revdep_details(, "glmGamPoi")
for more info
checking whether package ‘glmGamPoi’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/glmGamPoi/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/glmGamPoi/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/glmGamPoi/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/glmGamPoi/new/glmGamPoi.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 14.0Mb
sub-directories of 1Mb or more:
doc 2.4Mb
libs 11.2Mb
Run revdep_details(, "GPUmatrix")
for more info
checking Rd cross-references ... WARNING ``` Package unavailable to check Rd xrefs: ‘speedglm’ Missing link or links in documentation object 'LR_GradientConjugate_gpumatrix.Rd': ‘Matrix-class’
Missing link or links in documentation object 'gpu.matrix-class.Rd': ‘Matrix-class’
Missing link or links in documentation object 'gpu.matrix.Rd': ‘Matrix-class’
Missing link or links in documentation object 'matrix-product.Rd': ‘%&%’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
Run revdep_details(, "GRaNIE")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘JASPAR2022’
checking installed package size ... NOTE
installed size is 12.8Mb
sub-directories of 1Mb or more:
doc 11.6Mb
checking R code for possible problems ... NOTE
.performIHW: no visible binding for global variable 'adj_pvalue'
Undefined global functions or variables:
adj_pvalue
Run revdep_details(, "graper")
for more info
checking whether package ‘graper’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/graper/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/graper/new/graper.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
doc 1.8Mb
libs 7.1Mb
Run revdep_details(, "GUIDEseq")
for more info
checking installed package size ... NOTE
installed size is 12.5Mb
sub-directories of 1Mb or more:
extdata 11.9Mb
checking dependencies in R code ... NOTE
':::' call which should be '::': ‘CRISPRseek:::translatePattern’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
plotTracks: warning in scale_x_continuous(label =
xaxis.lab.pos$chromosome, breaks = xaxis.lab.pos$chr.center): partial
argument match of 'label' to 'labels'
.maskSubSeq: no visible global function definition for ‘.getMatchedInd’
.nucleotideSubstitutionMatrix: no visible binding for global variable
‘IUPAC_CODE_MAP’
.nucleotideSubstitutionMatrix: no visible binding for global variable
‘DNA_BASES’
GUIDEseqAnalysis: no visible binding for global variable ‘offTarget’
GUIDEseqAnalysis: no visible binding for global variable ‘peak_score’
...
feature gRNA.deletion gRNA.insertion gRNA.name gRNAPlusPAM
geom_smooth guideAlignment2OffTarget guide_legend guides h
mismatch.distance2PAM n.DNA.bulge n.PAM.mismatch n.RNA.bulge
n.deletion n.distinct.UMIs n.guide.mismatch n.insertion offTarget
offTargetStrand offTarget_End offTarget_Start offTarget_sequence
pa.f1 pa.r2 peak_score pos.deletion pos.insertion
predicted_cleavage_score qwidth.first qwidth.last readName
seqnames.first seqnames.last start.first start.last strand.first
strand.last thePeak total.mismatch.bulge unit width.first width.last
y
checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:35-37: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:63-65: Dropping empty section \references
prepare_Rd: createBarcodeFasta.Rd:56-58: Dropping empty section \references
prepare_Rd: getUsedBarcodes.Rd:53-55: Dropping empty section \references
checkRd: (-1) mergePlusMinusPeaks.Rd:72: Escaped LaTeX specials: \_
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘GUIDEseq.Rnw’ using Sweave Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘GUIDEseq.Rnw’
SUMMARY: processing the following file failed: ‘GUIDEseq.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "Gviz")
for more info
installed size is 9.8Mb
sub-directories of 1Mb or more:
R 1.7Mb
doc 4.8Mb
extdata 2.5Mb
Run revdep_details(, "GWENA")
for more info
checking whether package ‘GWENA’ can be installed ... WARNING
Found the following significant warnings:
Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/GWENA/new/GWENA.Rcheck/00install.out’ for details.
checking Rd files ... WARNING
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
checking installed package size ... NOTE
installed size is 8.0Mb
sub-directories of 1Mb or more:
data 2.3Mb
doc 5.4Mb
Run revdep_details(, "HACSim")
for more info
checking whether package ‘HACSim’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/HACSim/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/HACSim/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/HACSim/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/HACSim/new/HACSim.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 1.9Mb
shiny 4.2Mb
Run revdep_details(, "Harman")
for more info
checking running R code from vignettes ... ``` ‘IntroductionToHarman.Rmd’ using ‘UTF-8’... failed WARNING Errors in running code in vignettes: when running code in ‘IntroductionToHarman.Rmd’ ... > library(msmsEDA) Loading required package: MSnbase Loading required package: mzR Loading required package: Rcpp Error: package or namespace load failed for ‘mzR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘ncdf4’
When sourcing ‘IntroductionToHarman.R’: Error: package ‘mzR’ could not be loaded Execution halted ```
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 2.8Mb
libs 2.3Mb
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘IntroductionToHarman.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-7-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-8-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-11-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-12-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-13-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-16-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-20-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/Harman/new/Harman.Rcheck/vign_test/Harman/vignettes/IntroductionToHarman_files/figure-html/unnamed-chunk-23-1.png" but not available. ... Quitting from lines at lines 804-810 [msms] (IntroductionToHarman.Rmd) Error: processing vignette 'IntroductionToHarman.Rmd' failed with diagnostics: package 'mzR' could not be loaded --- failed re-building ‘IntroductionToHarman.Rmd’
SUMMARY: processing the following file failed: ‘IntroductionToHarman.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "hbamr")
for more info
checking installed package size ... NOTE
installed size is 355.3Mb
sub-directories of 1Mb or more:
libs 353.7Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "HDSpatialScan")
for more info
checking whether package ‘HDSpatialScan’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/HDSpatialScan/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/HDSpatialScan/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/HDSpatialScan/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/HDSpatialScan/new/HDSpatialScan.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
libs 5.8Mb
Run revdep_details(, "hermes")
for more info
checking tests ... ``` Running ‘test_dplyr_compatibility.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: Loading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
... 1. └─hermes::connect_biomart("GeneID") at test-connections.R:27:3 2. ├─base::tryCatch(...) 3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. ├─base::withCallingHandlers(...) 5. └─biomaRt::useEnsembl("ensembl", version = version) 6. └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, httr_config = httr_config)
[ FAIL 1 | WARN 2 | SKIP 16 | PASS 839 ] Error: Test failures Execution halted ```
Run revdep_details(, "hipathia")
for more info
checking installed package size ... NOTE
installed size is 10.6Mb
sub-directories of 1Mb or more:
data 4.1Mb
doc 1.8Mb
extdata 4.4Mb
checking R code for possible problems ... NOTE
DAreport: no visible binding for global variable ‘ID’
DAreport: no visible binding for global variable ‘FDRp.value’
DAtop : <anonymous>: no visible binding for global variable
‘FDRp.value’
DAtop : <anonymous>: no visible binding for global variable ‘statistic’
DAtop : <anonymous>: no visible binding for global variable ‘p.value’
DAtop : <anonymous>: no visible binding for global variable ‘name’
DAtop : <anonymous>: no visible binding for global variable ‘logPV’
DAtop : <anonymous>: no visible binding for global variable ‘feature’
DAtop: no visible binding for global variable ‘name’
...
summary_plot: no visible binding for global variable ‘UP.nodes’
summary_plot: no visible binding for global variable ‘DOWN.nodes’
summary_plot: no visible binding for global variable ‘nodes’
summary_plot: no visible binding for global variable ‘ratio.sigs’
summary_plot: no visible binding for global variable ‘ratio.UPs’
summary_plot: no visible binding for global variable ‘ratio.DOWNs’
Undefined global functions or variables:
DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction
feature from functional logPV name nodes p.value ratio.DOWNs
ratio.UPs ratio.sigs statistic status to total type value variable
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘hipathia-vignette.Rmd’ using rmarkdown createTcpServer: address already in use
Quitting from lines at lines 775-776 [unnamed-chunk-36] (hipathia-vignette.Rmd) Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics: Failed to create server --- failed re-building ‘hipathia-vignette.Rmd’
SUMMARY: processing the following file failed: ‘hipathia-vignette.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "iNETgrate")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘iNETgrate_inference.Rnw’ using knitr
Error: processing vignette 'iNETgrate_inference.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'iNETgrate_inference.tex' failed.
LaTeX errors:
! LaTeX Error: File
commath.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.48 ^^M
! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘iNETgrate_inference.Rnw’
SUMMARY: processing the following file failed: ‘iNETgrate_inference.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "InfiniumPurify")
for more info
Package unavailable to check Rd xrefs: ‘minfi’
Run revdep_details(, "IntOMICS")
for more info
checking running R code from vignettes ... ``` ‘IntOMICS_vignette.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘IntOMICS_vignette.Rmd’ ... Attaching package: ‘HDF5Array’
The following object is masked from ‘package:rhdf5’:
h5ls
When sourcing ‘IntOMICS_vignette.R’: Error: HDF5. File accessibility. Unable to open file. Execution halted ```
Warning: package needs dependence on R (>= 2.10)
Run revdep_details(, "iPath")
for more info
checking whether package ‘iPath’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/iPath/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/iPath/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/iPath/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/iPath/new/iPath.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking R code for possible problems ... NOTE
water_fall: no visible binding for global variable ‘value’
water_fall: no visible binding for global variable ‘type’
Undefined global functions or variables:
type value
Run revdep_details(, "JMbayes2")
for more info
checking whether package ‘JMbayes2’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/JMbayes2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/JMbayes2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/JMbayes2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/JMbayes2/new/JMbayes2.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 11.6Mb
sub-directories of 1Mb or more:
libs 10.9Mb
Run revdep_details(, "kgschart")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "kissDE")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘kissDE.rnw’ using Sweave Pre-processing the data... Trying to fit models on data... This can be a time-consuming step, so do not hesitate to have a look at the very well-written vignette ! Computing pvalues... Computing size of the effect and last cutoffs... Pre-processing the data... Trying to fit models on data... ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘kissDE.rnw’
SUMMARY: processing the following file failed: ‘kissDE.rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "LDM")
for more info
checking examples ... ERROR ``` Running examples in ‘LDM-Ex.R’ failed The error most likely occurred in:
Name: ldm
Title: Testing hypotheses about the microbiome using a linear
decomposition model (LDM)
Aliases: ldm
Keywords: microbiome
** Examples
res.ldm <- ldm(formula=throat.otu.tab5 | (Sex+AntibioticUse) ~ SmokingStatus+PackYears, + data=throat.meta, seed=67817, fdr.nominal=0.1, n.perm.max=1000, n.cores=1, + verbose=FALSE) Error: [matrixStats] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank() Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("LDM") Loading required package: LDM [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════ ... ▆ 1. └─LDM::ldm(...) at test-ldm.R:10:5 2. ├─base::array(colRanks(mat), c(n.var1, n.otu.smallp, n.perm.completed)) 3. └─matrixStats::colRanks(mat) 4. └─matrixStats:::tiesMethodMissing() 5. └─base (local) action(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted ```
Run revdep_details(, "ldsep")
for more info
checking whether package ‘ldsep’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/ldsep/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/ldsep/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/ldsep/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ldsep/new/ldsep.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
libs 8.3Mb
Run revdep_details(, "lemur")
for more info
checking whether package ‘lemur’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/lemur/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/lemur/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/lemur/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/lemur/new/lemur.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
data 2.6Mb
doc 1.1Mb
libs 2.6Mb
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
harmony_init: no visible global function definition for
‘packageVersion’
Undefined global functions or variables:
packageVersion
Consider adding
importFrom("utils", "packageVersion")
to your NAMESPACE file.
Run revdep_details(, "LFDREmpiricalBayes")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave
Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'LFDREmpiricalBayes.tex' failed.
LaTeX errors:
! LaTeX Error: File
changepage.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.10 \usepackage {url}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘LFDREmpiricalBayes.Rnw’
SUMMARY: processing the following file failed: ‘LFDREmpiricalBayes.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "liger")
for more info
checking whether package ‘liger’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/liger/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/liger/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/liger/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/liger/new/liger.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 3.3Mb
doc 2.1Mb
libs 2.2Mb
Run revdep_details(, "Linnorm")
for more info
checking whether package ‘Linnorm’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/Linnorm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/Linnorm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/Linnorm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/Linnorm/new/Linnorm.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 2.3Mb
doc 1.9Mb
libs 1.5Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘Linnorm_User_Manual.Rmd’ using rmarkdown
! LaTeX Error: File
titling.sty' not found.
! Emergency stop.
Error: processing vignette 'Linnorm_User_Manual.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/Linnorm/new/Linnorm.Rcheck/vign_test/Linnorm/vignettes/Linnorm_User_Manual.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Linnorm_User_Manual.log for more info. --- failed re-building ‘Linnorm_User_Manual.Rmd’
SUMMARY: processing the following file failed: ‘Linnorm_User_Manual.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "loo")
for more info
Run revdep_details(, "LSAmitR")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘kerdiest’
checking data for non-ASCII characters ... NOTE
Note: found 55 marked UTF-8 strings
Run revdep_details(, "lspartition")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "Luminescence")
for more info
checking whether package ‘Luminescence’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/Luminescence/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/Luminescence/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/Luminescence/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/Luminescence/new/Luminescence.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
R 1.6Mb
libs 3.5Mb
Run revdep_details(, "M3Drop")
for more info
checking installed package size ... NOTE
installed size is 12.9Mb
sub-directories of 1Mb or more:
doc 12.6Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘scater’
All declared Imports should be used.
checking R code for possible problems ... NOTE
M3DropConvertData: no visible global function definition for ‘assays’
NBumiConvertData: no visible global function definition for ‘assays’
bg__filter_cells: no visible binding for global variable ‘x’
bg__get_extreme_residuals: no visible binding for global variable ‘x’
Undefined global functions or variables:
assays x
checking Rd files ... NOTE
prepare_Rd: NBumi_FSOther.Rd:8-10: Dropping empty section \usage
prepare_Rd: NBumi_TradDE.Rd:7-8: Dropping empty section \usage
Run revdep_details(, "maEndToEnd")
for more info
checking DESCRIPTION meta-information ... WARNING
Invalid license file pointers: LICENSE
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase', 'oligoClasses', 'ArrayExpress', 'pd.hugene.1.0.st.v1',
'hugene10sttranscriptcluster.db', 'oligo', 'arrayQualityMetrics',
'limma', 'topGO', 'ReactomePA', 'clusterProfiler', 'gplots',
'ggplot2', 'geneplotter', 'pheatmap', 'RColorBrewer', 'dplyr',
'tidyr', 'stringr', 'matrixStats', 'genefilter', 'openxlsx',
'Rgraphviz', 'enrichplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 6.1Mb
checking top-level files ... NOTE
File
LICENCE
is not mentioned in the DESCRIPTION file.
checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘AnnotationDbi’
Run revdep_details(, "magpie")
for more info
'::' or ':::' import not declared from: ‘htmltools’
Run revdep_details(, "MatrixGenerics")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MatrixGenerics) Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
... Error: [matrixStats] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank() Backtrace: ▆ 1. └─matrixStats::rowRanks(x = mat) at test-api_compatibility.R:1207:9 2. └─matrixStats:::tiesMethodMissing() 3. └─base (local) action(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 374 ] Error: Test failures Execution halted ```
Unexported objects imported by ':::' calls:
‘methods:::fromNextMethod’ ‘methods:::getGenericFromCall’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.load_next_suggested_package_to_search’
Run revdep_details(, "mcmcsae")
for more info
installed size is 27.7Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 26.1Mb
Run revdep_details(, "MEAL")
for more info
checking running R code from vignettes ... ``` ‘MEAL.Rmd’ using ‘UTF-8’... failed ‘caseExample.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘MEAL.Rmd’ ...
targetRange <- GRanges("chrX:13000000-14000000")
plotRegion(resAdj, targetRange) ... plot(gexpRes, rid = "DiffMean", type = "manhattan", + main = "Differences in Means", highlight = targetRangeNum)
plotRegion(rset = methRes, rset2 = gexpRes, range = targetRange) Warning in curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) : Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x318a75c0): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
When sourcing 'caseExample.R': Error: attempt to set an attribute on NULL Execution halted ```
checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'sva'
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'getProbeResults' ‘robust’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking examples ... WARNING ``` Found the following significant warnings:
Warning: 'runRegionAnalysis' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE
plotRegion: no visible global function definition for
‘subsetByOverlaps’
plotRegion: no visible global function definition for ‘mcols<-’
runRDA: no visible global function definition for ‘rowData’
runSVA: no visible global function definition for ‘resid’
runSVA: no visible global function definition for ‘quantile’
Undefined global functions or variables:
mcols<- quantile resid rowData subsetByOverlaps
Consider adding
importFrom("stats", "quantile", "resid")
to your NAMESPACE file.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘DMRcate’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘MEAL.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 1-2.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Volcano 1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/QQ-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Plot_Features-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Plot_Features-2.png" but not available.
... Quitting from lines at lines 157-158 [Regional plot 2 exp] (caseExample.Rmd) Error: processing vignette 'caseExample.Rmd' failed with diagnostics: attempt to set an attribute on NULL --- failed re-building ‘caseExample.Rmd’
SUMMARY: processing the following files failed: ‘MEAL.Rmd’ ‘caseExample.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "memes")
for more info
checking running R code from vignettes ... ``` ‘core_ame.Rmd’ using ‘UTF-8’... failed ‘core_dreme.Rmd’ using ‘UTF-8’... failed ‘core_fimo.Rmd’ using ‘UTF-8’... failed ‘core_tomtom.Rmd’ using ‘UTF-8’... OK ‘install_guide.Rmd’ using ‘UTF-8’... OK ‘integrative_analysis.Rmd’ using ‘UTF-8’... failed ‘tidy_motifs.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: when running code in ‘core_ame.Rmd’ ... [["orphan"]] chr3L:57749-57848=GAAACCTATACCCCGCCGTCGGCCGATTATCACCTTTTCAAGTCTC...
ame_by_binding <- by_binding %>% runAme
When sourcing ‘integrative_analysis.R’:
Error: ℹ In index: 1.
ℹ With name: ectopic.
Caused by error in .check_valid_command_path()
:
! Command: /c4/home/henrik/meme/bin, does not exist.
Execution halted
```
checking S3 generic/method consistency ... WARNING ``` motif_input: function(x, ...) motif_input.universalmotif_df: function(input, path)
motif_input: function(x, ...) motif_input.universalmotif: function(input, path)
... function(x) sequence_input.BStringSet: function(input)
sequence_input: function(x) sequence_input.AAStringSet: function(input) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "metagene")
for more info
checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 50 lines of output: [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq produce data table : ChIP-Seq ChIP-Seq flip/unflip ...
test_parallel_job.R
test.parallel_job_get_core_count_valid_multiple_core_biocparallelparam
test.parallel_job_set_core_count_valid_multiple_core_biocparallelparam
Error in BiocGenerics:::testPackage("metagene") : unit tests failed for package metagene In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted ```
checking Rd files ... WARNING
checkRd: (5) Bam_Handler.Rd:22: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:42: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:46: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:50: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:54: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:58: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:61-62: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:71-72: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:81: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:23-26: \item in \describe must have non-empty label
...
checkRd: (5) metagene.Rd:130: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:133: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:144: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:147: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:155: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:164: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:170: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:179: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:183: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:186: \item in \describe must have non-empty label
checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
doc 3.2Mb
extdata 5.3Mb
checking R code for possible problems ... NOTE
NCIS.internal: no visible global function definition for
'est.norm.med.search'
avoid_gaps_update: no visible binding for global variable 'value'
avoid_gaps_update: no visible binding for global variable 'bam'
avoid_gaps_update: no visible binding for global variable 'tab'
avoid_gaps_update: no visible binding for global variable 'nuc'
bin.data: no visible global function definition for 'hist'
permutation_test: no visible global function definition for '.'
permutation_test: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'bin'
...
plot_metagene: no visible binding for global variable 'group'
plot_metagene: no visible binding for global variable 'nuc'
plot_metagene: no visible binding for global variable 'design'
plot_metagene: no visible binding for global variable 'nuctot'
Undefined global functions or variables:
. bam bin design est.norm.med.search group hist nuc nuctot qinf qsup
tab value
Consider adding
importFrom("graphics", "hist")
to your NAMESPACE file.
Run revdep_details(, "metagenomeSeq")
for more info
checking running R code from vignettes ... ``` ‘fitTimeSeries.Rnw’... OK ‘metagenomeSeq.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘metagenomeSeq.Rnw’ ... [5] "Campylobacter curvus" [6] "Prevotella intermedia"
classes = pData(mouseData)$diet
res = fitPA(mouseData[1:5, ], cl = classes)
When sourcing ‘metagenomeSeq.R’: Error: creation of server socket failed: port 11150 cannot be opened Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: > # but now you have the flexibility as requested by CRAN maintainers. > test_check("metagenomeSeq") Loading required package: metagenomeSeq Loading required package: Biobase Loading required package: BiocGenerics
...
── Failure ('test-norm.R:28:3'): cumNormStat
returns the correct value ───────
cumNormStat(lungData) not equal to 0.7014946.
names for target but not for current
── Failure ('test-norm.R:34:3'): cumNormStatFast
returns the correct value ───
cumNormStatFast(lungData) not equal to 0.7014946.
names for target but not for current
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted ```
Run revdep_details(, "metamicrobiomeR")
for more info
Namespace in Imports field not imported from: ‘lmerTest’
All declared Imports should be used.
Run revdep_details(, "MetaNeighbor")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘MetaNeighbor.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'MetaNeighbor.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/MetaNeighbor/new/MetaNeighbor.Rcheck/vign_test/MetaNeighbor/vignettes/MetaNeighbor.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MetaNeighbor.log for more info. --- failed re-building ‘MetaNeighbor.Rmd’
SUMMARY: processing the following file failed: ‘MetaNeighbor.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "MethReg")
for more info
checking examples ... ERROR ``` Running examples in ‘MethReg-Ex.R’ failed The error most likely occurred in:
Name: create_triplet_distance_based
Title: Map DNAm to target genes using distance approaches, and TF to
the DNAm region using JASPAR2020 TFBS.
Aliases: create_triplet_distance_based
** Examples
... + motif.search.window.size = 500, + target.method = "closest.gene" + ) Finding target genes Removing regions overlapping promoter regions o Get promoter regions for hg38 o Remove promoter regions Looking for TFBS Error: JASPAR2022 package is needed for this function to work. Please install it. Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:
| | 0% |====================================================|100% ~0 s remaining |====================================================|100% Completed after 2 s
| | 0% ... Backtrace: ▆ 1. └─MethReg::get_tf_in_region(...) at test-get_tf_in_region.R:18:5 2. └─MethReg:::check_package("JASPAR2022") 3. └─base::suppressMessages(...) 4. └─base::withCallingHandlers(...)
[ FAIL 2 | WARN 4 | SKIP 3 | PASS 156 ] Error: Test failures Execution halted ```
checking running R code from vignettes ... ``` ‘MethReg.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘MethReg.Rmd’ ... > triplet.promoter <- create_triplet_distance_based(region = dna.met.chr21.se,
When sourcing ‘MethReg.R’: Error: JASPAR2022 package is needed for this function to work. Please install it. Execution halted ```
checking dependencies in R code ... WARNING
Missing or unexported object: ‘downloader::download.file’
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘JASPAR2022’
checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
R 1.6Mb
doc 2.5Mb
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘downloader’
A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE
readRemap2022: no visible binding for global variable ‘biotype’
Undefined global functions or variables:
biotype
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘TCGAbiolinks’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘MethReg.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MethReg/new/MethReg.Rcheck/vign_test/MethReg/vignettes/MethReg_files/figure-html/workflow-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MethReg/new/MethReg.Rcheck/vign_test/MethReg/vignettes/MethReg_files/figure-html/plot-1.png" but not available.
Quitting from lines at lines 323-333 [unnamed-chunk-9] (MethReg.Rmd) Error: processing vignette 'MethReg.Rmd' failed with diagnostics: JASPAR2022 package is needed for this function to work. Please install it. --- failed re-building ‘MethReg.Rmd’
SUMMARY: processing the following file failed: ‘MethReg.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "methrix")
for more info
extract_CPGs: no visible global function definition for
‘standardChromosomes’
get_region_summary: no visible binding for global variable ‘..keep’
Undefined global functions or variables:
..keep standardChromosomes
Run revdep_details(, "MethylAid")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘MethylAidData’
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘MethylAid.Rnw’ using knitr
Error: processing vignette 'MethylAid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'MethylAid.tex' failed.
LaTeX errors:
! LaTeX Error: File
nowidow.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MethylAid.Rnw’
SUMMARY: processing the following file failed: ‘MethylAid.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "methylationArrayAnalysis")
for more info
checking running R code from vignettes ... ``` ‘methylationArrayAnalysis.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘methylationArrayAnalysis.Rmd’ ... > par(mfrow = c(1, 1))
DMR.plot(ranges = results.ranges, dmr = 2, CpGs = bVals, + phen.col = cols, what = "Beta", arraytype = "450K", genome = "hg19") Warning in curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) : Error setting the option for # 3 (status = 43) (enum = 81) (value = 0xbdaa7a10): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
When sourcing 'methylationArrayAnalysis.R': Error: attempt to set an attribute on NULL Execution halted ```
checking whether package ‘methylationArrayAnalysis’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'rmarkdown::pdf_document' by 'BiocStyle::pdf_document' when loading 'methylationArrayAnalysis'
Warning: replacing previous import 'rmarkdown::html_document' by 'BiocStyle::html_document' when loading 'methylationArrayAnalysis'
Warning: replacing previous import 'rmarkdown::md_document' by 'BiocStyle::md_document' when loading 'methylationArrayAnalysis'
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'knitr', 'rmarkdown', 'BiocStyle', 'limma', 'minfi',
'IlluminaHumanMethylation450kanno.ilmn12.hg19',
'IlluminaHumanMethylation450kmanifest', 'RColorBrewer', 'missMethyl',
'matrixStats', 'minfiData', 'Gviz', 'DMRcate', 'stringr',
'FlowSorted.Blood.450k'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 322.7Mb
sub-directories of 1Mb or more:
doc 2.6Mb
extdata 320.2Mb
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘methylationArrayAnalysis.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure3-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure4-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure5-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure6-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure7-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure8-1.png" but not available. ... Quitting from lines at lines 461-465 [figure10] (methylationArrayAnalysis.Rmd) Error: processing vignette 'methylationArrayAnalysis.Rmd' failed with diagnostics: attempt to set an attribute on NULL --- failed re-building ‘methylationArrayAnalysis.Rmd’
SUMMARY: processing the following file failed: ‘methylationArrayAnalysis.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "methylumi")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase', 'scales', 'reshape2', 'ggplot2', 'matrixStats',
'FDb.InfiniumMethylation.hg19', 'minfi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 11.8Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 2.7Mb
doc 1.9Mb
extdata 5.8Mb
checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’
A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’
‘reshape2’ ‘scales’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
...
Packages in Depends field not imported from:
‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’
‘reshape2’ ‘scales’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
getBarcodes: warning in list.files(path = path, patt = "idat"): partial
argument match of 'patt' to 'pattern'
coerce,RangedSummarizedExperiment-GenomicMethylSet: warning in
assays(from, withDim = F): partial argument match of 'withDim' to
'withDimnames'
.getFinalReportBlock: no visible global function definition for
‘read.table’
.mclapply: no visible global function definition for ‘mclapply’
.parallel : <anonymous>: no visible global function definition for
‘ecdf’
...
subsetCommonProbes text theme_bw title value variable weighted.mean
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("graphics", "abline", "axis", "box", "lines", "par",
"points", "rect", "text", "title")
importFrom("stats", "as.dist", "dnorm", "ecdf", "hclust", "offset",
"p.adjust", "pnorm", "weighted.mean")
importFrom("utils", "capture.output", "data", "packageDescription",
"packageVersion", "read.csv", "read.delim", "read.table")
to your NAMESPACE file.
checking Rd files ... NOTE
prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso
prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples
checkRd: (-1) extractBarcodeAndPosition.Rd:14: Escaped LaTeX specials: \_ \_
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Run revdep_details(, "microbiomeExplorer")
for more info
installed size is 12.5Mb
sub-directories of 1Mb or more:
doc 5.0Mb
extdata 4.1Mb
shiny 2.8Mb
Run revdep_details(, "microsamplingDesign")
for more info
checking whether package ‘microsamplingDesign’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/microsamplingDesign/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/microsamplingDesign/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/microsamplingDesign/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/microsamplingDesign/new/microsamplingDesign.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘microsamplingDesign.Rmd’ using rmarkdown
Warning: The closing fence on line 165 ("
") in microsamplingDesign.Rmd does not match the opening fence " ``" on line 163. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/microsamplingDesign/new/microsamplingDesign.Rcheck/vign_test/microsamplingDesign/vignettes/microsamplingDesign.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See microsamplingDesign.log for more info. --- failed re-building ‘microsamplingDesign.Rmd’
SUMMARY: processing the following file failed: ‘microsamplingDesign.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "migest")
for more info
Note: found 9 marked UTF-8 strings
Run revdep_details(, "miloR")
for more info
checking running R code from vignettes ... ``` ‘milo_contrasts.Rmd’ using ‘UTF-8’... failed ‘milo_demo.Rmd’ using ‘UTF-8’... OK ‘milo_gastrulation.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: when running code in ‘milo_contrasts.Rmd’ ... hub path: ‘https://experimenthub.bioconductor.org/fetch/4641’ cache resource: ‘EH4598 : 4641’ reason: bfcadd() failed; see warnings()
When sourcing ‘milo_contrasts.R’: Error: failed to load resource name: EH4598 title: SMARTseq colData (day 1) reason: 1 resources failed to download Execution halted ```
checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
data 1.8Mb
doc 5.4Mb
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
.fromMatrix: no visible binding for global variable ‘sce’
plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’
plotDAbeeswarm: no visible binding for global variable ‘logFC’
plotDAbeeswarm: no visible binding for global variable ‘is_signif’
plotDAbeeswarm: no visible binding for global variable ‘Nhood’
plotDAbeeswarm: no visible binding for global variable ‘logFC_color’
plotNhoodCounts: no visible binding for global variable ‘values’
plotNhoodCounts: no visible binding for global variable ‘..y..’
plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’
plotNhoodExpressionDA: no visible binding for global variable ‘logFC’
...
plotNhoodMA: no visible binding for global variable ‘logFC’
plotNhoodMA: no visible binding for global variable ‘Sig’
plotNhoodSizeHist: no visible binding for global variable ‘nh_size’
Undefined global functions or variables:
. ..y.. Nhood NhoodGroup Sig SpatialFDR avg_expr feature is_signif
label layout logCPM logFC logFC_color logFC_rank nh_size sce size
values weight
Consider adding
importFrom("graphics", "layout")
to your NAMESPACE file.
Run revdep_details(, "MinimumDistance")
for more info
checking whether package ‘MinimumDistance’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/MinimumDistance/new/MinimumDistance.Rcheck/00install.out’ for details.
checking Rd files ... WARNING
checkRd: (5) MinimumDistance.Rd:0-7: Must have a \description
checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'coerce' but not in code:
‘as’
checking Rd \usage sections ... WARNING ``` Objects in \usage without \alias in documentation object 'coerce': ‘as’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking contents of ‘data’ directory ... WARNING
Output for data("trioSetListExample", package = "MinimumDistance"):
Warning message:
replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doSNOW’
checking startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘MatrixGenerics’
All declared Imports should be used.
checking R code for possible problems ... NOTE
callDenovoSegments: no visible global function definition for
‘read.bsfiles’
combineRanges: no visible global function definition for ‘RangedData’
getRefGene: no visible global function definition for ‘RangedData’
overlapsCentromere: no visible global function definition for
‘RangedData’
pruneMD: no visible global function definition for ‘RangedDataCBS’
pruneTrioSet: no visible global function definition for
‘RangedDataList’
read.bsfiles2: no visible binding for global variable ‘read.bsfiles’
GenomeAnnotatedDataFrameFrom,character: no visible global function
definition for ‘read.bsfiles’
calculateMindist,list: no visible binding for global variable ‘elt’
Undefined global functions or variables:
RangedData RangedDataCBS RangedDataList elt read.bsfiles
Run revdep_details(, "mixOmics")
for more info
checking running R code from vignettes ... ``` ‘vignette.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘vignette.Rmd’ ... > plotIndiv(final.plsda.srbct, ind.names = FALSE, legend = TRUE,
knitr::include_graphics(c("Figures/PLSDA/05-plsda-sample-plot-nc12-1.png", + "Figures/PLSDA/05-plsda-sample-plot-nc13-1.png"))
When sourcing ‘vignette.R’: Error: Cannot find the file(s): "Figures/PLSDA/05-plsda-sample-plot-nc12-1.png"; "Figures/PLSDA/05-plsda-sample-plot-nc13-1.png" Execution halted ```
checking installed package size ... NOTE
installed size is 23.2Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 3.3Mb
doc 17.1Mb
Run revdep_details(, "mnem")
for more info
installed size is 10.3Mb
sub-directories of 1Mb or more:
data 2.3Mb
doc 3.8Mb
libs 3.8Mb
Run revdep_details(, "moanin")
for more info
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘edge’
Unknown package ‘KEGGprofile’ in Rd xrefs
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘documentation.Rmd’ using knitr
Quitting from lines at lines 45-49 [unnamed-chunk-2] (documentation.Rmd) Error: processing vignette 'documentation.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘documentation.Rmd’
SUMMARY: processing the following file failed: ‘documentation.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "MOCHA")
for more info
checking running R code from vignettes ... ``` ‘COVID-walkthrough.Rmd’ using ‘UTF-8’... failed ‘ImportingFromOtherSources.Rmd’ using ‘UTF-8’... failed WARNING Errors in running code in vignettes: when running code in ‘COVID-walkthrough.Rmd’ ... > knitr::opts_chunk$set(collapse = TRUE, comment = "#>",
library(MOCHA) ... ...
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", + eval = FALSE)
library(Signac)
When sourcing ‘ImportingFromOtherSources.R’: Error: there is no package called ‘Signac’ Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ArchR’
Run revdep_details(, "monocle")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Rcpp’ ‘biocViews’
All declared Imports should be used.
checking R code for possible problems ... NOTE
assign_cell_lineage: no visible global function definition for ‘nei’
buildBranchCellDataSet: no visible global function definition for ‘nei’
count_leaf_descendents: no visible global function definition for ‘nei’
cth_classifier_cds: no visible global function definition for ‘nei’
cth_classifier_cell: no visible global function definition for ‘nei’
diff_test_helper: no visible binding for global variable ‘Size_Factor’
exportCDS: no visible binding for global variable ‘use_for_ordering’
extract_good_ordering: no visible global function definition for ‘nei’
fit_model_helper: no visible binding for global variable ‘Size_Factor’
get_next_node_id: no visible binding for '<<-' assignment to
...
variable ‘Branch’
project2MST: no visible global function definition for ‘nei’
reverseEmbeddingCDS : <anonymous>: no visible global function
definition for ‘quantile’
Undefined global functions or variables:
Branch Size_Factor nei next_node pseudocount quantile
use_for_ordering
Consider adding
importFrom("stats", "quantile")
to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘monocle-vignette.Rnw’ using knitr
Error: processing vignette 'monocle-vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'monocle-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File
sectsty.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.37 \sectionfont {\sffamily\bfseries\color{RoyalBlue}\sectionrule{0pt}{0pt}{... ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘monocle-vignette.Rnw’
SUMMARY: processing the following file failed: ‘monocle-vignette.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "MOSim")
for more info
checking running R code from vignettes ... ``` ‘MOSim.Rnw’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘MOSim.Rnw’ ...
rnaseq_simulation <- mosim(omics = c("RNA-seq"), times = 0, + numberGroups = 1, numberReps = 4)
When sourcing ‘MOSim.R’: Error: invalid class “MOSimulation” object: The design must have a minimum of 2 times or 2 groups. Execution halted ```
checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 4.2Mb
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘MOSim.Rnw’ using knitr
Quitting from lines at lines 245-271 [code6] (MOSim.Rnw) Error: processing vignette 'MOSim.Rnw' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘MOSim.Rnw’
SUMMARY: processing the following file failed: ‘MOSim.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "motifbreakR")
for more info
checking for missing documentation entries ... WARNING
Undocumented data sets:
'example.pvalue'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'MotifDb'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking data for non-ASCII characters ... NOTE
Note: found 6 marked UTF-8 strings
Run revdep_details(, "mrfDepth")
for more info
checking whether package ‘mrfDepth’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/mrfDepth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/mrfDepth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/mrfDepth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/mrfDepth/new/mrfDepth.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 22.5Mb
sub-directories of 1Mb or more:
data 1.6Mb
libs 20.6Mb
Run revdep_details(, "msqrob2")
for more info
checking running R code from vignettes ... ``` ‘cptac.Rmd’ using ‘UTF-8’... failed WARNING Errors in running code in vignettes: when running code in ‘cptac.Rmd’ ... > rowData(pe[["peptideRaw"]])$nNonZero <- rowSums(assay(pe[["peptideRaw"]]) >
pe <- zeroIsNA(pe, "peptideRaw")
MSnbase::plotNA(assay(pe[["peptideRaw"]])) + xlab("Peptide index (ordered by data completeness)")
When sourcing ‘cptac.R’: Error: there is no package called ‘ncdf4’ Execution halted ```
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘cptac.Rmd’ using rmarkdown
Quitting from lines at lines 119-121 [unnamed-chunk-5] (cptac.Rmd) Error: processing vignette 'cptac.Rmd' failed with diagnostics: there is no package called 'ncdf4' --- failed re-building ‘cptac.Rmd’
SUMMARY: processing the following file failed: ‘cptac.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "MultiBD")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 10.3Mb
sub-directories of 1Mb or more:
libs 8.8Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘SIR-MCMC.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'SIR-MCMC.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/MultiBD/new/MultiBD.Rcheck/vign_test/MultiBD/vignettes/SIR-MCMC.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SIR-MCMC.log for more info. --- failed re-building ‘SIR-MCMC.Rmd’ ... l.75 \usepackage {amsmath}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘SIRtrans.Rnw’
SUMMARY: processing the following files failed: ‘SIR-MCMC.Rmd’ ‘SIRtrans.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "multinomialLogitMix")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/multinomialLogitMix/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/multinomialLogitMix/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/multinomialLogitMix/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/multinomialLogitMix/new/multinomialLogitMix.Rcheck/00install.out’ for details.
Run revdep_details(, "muscat")
for more info
checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
doc 6.0Mb
checking R code for possible problems ... NOTE
pbHeatmap: no visible binding for global variable ‘gene’
pbHeatmap: no visible binding for global variable ‘p_adj.loc’
pbHeatmap: no visible binding for global variable ‘logFC’
Undefined global functions or variables:
gene logFC p_adj.loc
Run revdep_details(, "muscData")
for more info
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘Crowell19_4vs4’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘SingleCellExperiment’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Run revdep_details(, "NanoStringDiff")
for more info
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘compute.baseSigma’ ‘est.dispersion’ ‘fun5’ ‘glmfit.OneGroup’
‘glmfit.full’ ‘glmfit.reduce’ ‘rnegbinom’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking installed files from ‘inst/doc’ ... NOTE
The following files look like leftovers/mistakes:
‘NanoStringDiff.log’
Please remove them from your package.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘NanoStringDiff.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
... l.37 \sectionfont {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-... ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘NanoStringDiff.Rnw’
SUMMARY: processing the following file failed: ‘NanoStringDiff.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "nearBynding")
for more info
checking running R code from vignettes ... ``` ‘nearBynding.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘nearBynding.Rmd’ ... [1] "knit_image_paths" "knit_asis"
bindingContextDistance(RNA_context = "chr4and5_3UTR_stem_liftOver", + protein_file = "chr4and5_liftOver", RNA_context_2 = "chr4and5_3UTR_hairpi ..." ... [TRUNCATED] Warning in file(file, "rt") : cannot open file './chr4and5_3UTR_stem_liftOver~chr4and5_liftOver.dist': No such file or directory
When sourcing ‘nearBynding.R’: Error: cannot open the connection Execution halted ```
checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
extdata 6.9Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘nearBynding.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'nearBynding.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/nearBynding/new/nearBynding.Rcheck/vign_test/nearBynding/vignettes/nearBynding.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See nearBynding.log for more info. --- failed re-building ‘nearBynding.Rmd’
SUMMARY: processing the following file failed: ‘nearBynding.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "netZooR")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [1] 187 [1] 188 [1] 189 [1] 190 [1] 191 [1] 192 ... Backtrace: ▆
[ FAIL 1 | WARN 9 | SKIP 1 | PASS 48 ] Error: Test failures Execution halted ```
checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 1.5Mb
extdata 2.8Mb
checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘matrixcalc’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE
estimatePenaltyParameters: no visible global function definition for
‘matrix.trace’
runEgret: no visible binding for global variable ‘NA12878’
show,panda: no visible global function definition for ‘print.panda’
Undefined global functions or variables:
NA12878 matrix.trace print.panda
Run revdep_details(, "nn2poly")
for more info
checking whether package ‘nn2poly’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/nn2poly/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/nn2poly/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/nn2poly/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/nn2poly/new/nn2poly.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++14: please drop specification unless essential
Run revdep_details(, "NormalyzerDE")
for more info
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Run revdep_details(, "numbat")
for more info
checking whether package ‘numbat’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/numbat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/numbat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/numbat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/numbat/new/numbat.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 4.2Mb
libs 1.2Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘R.utils’ ‘optparse’ ‘vcfR’
All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "omicplotR")
for more info
Package in Depends field not imported from: ‘ALDEx2’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Run revdep_details(, "omicsPrint")
for more info
checking LazyData ... WARNING
LazyData DB of 7.3 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
checking installed package size ... NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
data 7.3Mb
doc 1.2Mb
Run revdep_details(, "omicsViewer")
for more info
installed size is 6.2Mb
sub-directories of 1Mb or more:
extdata 4.8Mb
Run revdep_details(, "OncoBayes2")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE
installed size is 87.0Mb
sub-directories of 1Mb or more:
libs 85.2Mb
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_blrm_exnex” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_blrm_exnex” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "OptimalDesign")
for more info
checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'gurobi', 'slam'
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "OUTRIDER")
for more info
checking whether package ‘OUTRIDER’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/OUTRIDER/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/OUTRIDER/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/OUTRIDER/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/OUTRIDER/new/OUTRIDER.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
doc 2.3Mb
libs 3.1Mb
checking R code for possible problems ... NOTE
padjOnSubset: no visible global function definition for ‘bpmapply’
Undefined global functions or variables:
bpmapply
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘OUTRIDER.Rnw’ using knitr The magick package is required to crop "figure/deVsOutlier-1.png" but not available. The magick package is required to crop "figure/quick_guide-1.png" but not available. The magick package is required to crop "figure/filtering-1.png" but not available. The magick package is required to crop "figure/filtering-2.png" but not available. The magick package is required to crop "figure/plotting_between_sample_correlations-1.png" but not available. The magick package is required to crop "figure/plotting_between_sample_correlations-2.png" but not available. The magick package is required to crop "figure/controlling_for_confounders-1.png" but not available. The magick package is required to crop "figure/aberrantperSample-1.png" but not available. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘OUTRIDER.Rnw’
SUMMARY: processing the following file failed: ‘OUTRIDER.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "pandaR")
for more info
checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
checking LazyData ... WARNING
LazyData DB of 9.0 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
checking installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
data 9.0Mb
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'summary.panda': ‘summary.panda’
The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "pARI")
for more info
checking whether package ‘pARI’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/pARI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/pARI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/pARI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/pARI/new/pARI.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 5.1Mb
Run revdep_details(, "PathoStat")
for more info
Namespaces in Imports field not imported from:
‘ComplexHeatmap’ ‘RColorBrewer’
All declared Imports should be used.
Run revdep_details(, "pcaMethods")
for more info
Package unavailable to check Rd xrefs: ‘ade4’
Run revdep_details(, "PDATK")
for more info
checking whether package ‘PDATK’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/PDATK/new/PDATK.Rcheck/00install.out’ for details.
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'rankFeatures-MultiAssayExperiment-method.Rd': ‘[dplyr:ranking]{dplyr::dense_rank}’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 3.3Mb
checking R code for possible problems ... NOTE
.calculateMSMthresholds: no visible binding for global variable
‘funContext’
.plotNetwork: no visible global function definition for ‘legend’
NCSModel: no visible binding for global variable ‘metric’
NCSModel: no visible binding for global variable ‘comparison’
NCSModel: no visible binding for global variable ‘centroid_K’
NCSModel: no visible binding for global variable ‘assay_K’
NetworkCommunitySearchModel: no visible binding for global variable
‘metric’
NetworkCommunitySearchModel: no visible binding for global variable
...
trainModel,NCSModel: no visible binding for global variable
‘cor_threshold’
Undefined global functions or variables:
.error assay_K assay_cohort centroid_K centroid_cohort cluster_label
comparison cor_threshold dev.off feature feature_rank feature_score
funContext ingroup_proportion legend metric missignAssays pdf tmp
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "legend")
to your NAMESPACE file.
Run revdep_details(, "pecora")
for more info
checking examples ... ERROR ``` Running examples in ‘pecora-Ex.R’ failed The error most likely occurred in:
Name: pecora-package
Title: pecora-package
Aliases: pecora-package pecora.package pecorapackage
Keywords: package
** Examples
X <- matrix(rnorm(100*20), nrow=20) out <- oneSample(X = X) pv <- t2p(Test = out, alternative = "two.sided") Error: [matrixStats] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank() Execution halted ```
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/pecora/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/pecora/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/pecora/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/pecora/new/pecora.Rcheck/00install.out’ for details.
Run revdep_details(, "penppml")
for more info
checking installed package size ... NOTE
installed size is 14.0Mb
sub-directories of 1Mb or more:
data 1.8Mb
libs 12.0Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘fixest’
All declared Imports should be used.
Run revdep_details(, "PepsNMR")
for more info
checkRd: (-1) Normalization.Rd:47: Escaped LaTeX specials: \&
Run revdep_details(, "pgKDEsphere")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/pgKDEsphere/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/pgKDEsphere/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/pgKDEsphere/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/pgKDEsphere/new/pgKDEsphere.Rcheck/00install.out’ for details.
Run revdep_details(, "phosphonormalizer")
for more info
Package which this enhances but not available for checking: ‘MSnbase’
Run revdep_details(, "Pigengene")
for more info
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ``` Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn")
one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db ```
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘Pigengene_inference.Rnw’ using knitr
Error: processing vignette 'Pigengene_inference.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Pigengene_inference.tex' failed.
LaTeX errors:
! LaTeX Error: File
nowidow.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘Pigengene_inference.Rnw’
SUMMARY: processing the following file failed: ‘Pigengene_inference.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "PINSPlus")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/PINSPlus/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/PINSPlus/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/PINSPlus/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/PINSPlus/new/PINSPlus.Rcheck/00install.out’ for details.
Run revdep_details(, "pipeComp")
for more info
checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 4.5Mb
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’
checking R code for possible problems ... NOTE
scrna_describeDatasets: no visible binding for global variable
‘cluster’
scrna_describeDatasets: no visible binding for global variable ‘nb’
scrna_describeDatasets : pf: no visible binding for global variable
‘.x’
scrna_describeDatasets : rd: no visible binding for global variable ‘y’
scrna_describeDatasets : rd: no visible binding for global variable
‘cluster’
scrna_evalPlot_filtering: no visible binding for global variable
‘max.lost’
...
scrna_evalPlot_filtering: no visible binding for global variable
‘doubletmethod’
scrna_evalPlot_filtering: no visible binding for global variable
‘method’
scrna_evalPlot_overall: no visible binding for global variable
‘true.nbClusts’
scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’
Undefined global functions or variables:
.x cluster doubletmethod filt max.lost mean_F1 method n_clus nb
true.nbClusts y
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
‘edgeR’ ‘sva’
Run revdep_details(, "PlackettLuce")
for more info
Package suggested but not available for checking: ‘PLMIX’
Run revdep_details(, "pmp")
for more info
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 1.8Mb
doc 5.6Mb
Run revdep_details(, "POMaSPU")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/POMaSPU/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/POMaSPU/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/POMaSPU/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/POMaSPU/new/POMaSPU.Rcheck/00install.out’ for details.
Run revdep_details(, "posterior")
for more info
checking running R code from vignettes ... ``` ‘posterior.Rmd’ using ‘UTF-8’... OK ‘rvar.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘rvar.Rmd’ ... > y rvar<4000>[3] mean ± sd: [1] 3.00 ± 1.00 2.02 ± 0.99 0.96 ± 0.99
X + y
When sourcing ‘rvar.R’: Error: Cannot broadcast array of shape [4000,3,1] to array of shape [4000,4,3]: All dimensions must be 1 or equal. Execution halted ```
Run revdep_details(, "ProteoDisco")
for more info
checking whether package ‘ProteoDisco’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ProteoDisco/new/ProteoDisco.Rcheck/00install.out’ for details.
checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'show' and siglist 'ProteoDiscography'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘ProteoDisco’ for: ‘show’
A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file. ```
checking data for non-ASCII characters ... NOTE ``` Error loading dataset 'ProteoDiscographyExample.hg19': Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed
```
Run revdep_details(, "ProteoMM")
for more info
License components which are templates and need '+ file LICENSE':
MIT
Run revdep_details(, "QDNAseq")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘QDNAseq.Rnw’ using Sweave EM algorithm started ...
Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead.
Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘QDNAseq.Rnw’
SUMMARY: processing the following file failed: ‘QDNAseq.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "QFeatures")
for more info
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'QFeatures-aggregate.Rd': ‘sparseMatrix’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
doc 4.3Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’
‘MultiAssayExperiment:::.sampleMapFromData’
See the note in ?`:::` about the use of this operator.
Run revdep_details(, "RaceID")
for more info
installed size is 11.8Mb
sub-directories of 1Mb or more:
data 2.1Mb
doc 6.7Mb
libs 2.2Mb
Run revdep_details(, "rADA")
for more info
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 5.5Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
All declared Imports should be used.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘rada_vignette.Rmd’ using knitr
Quitting from lines at lines 62-70 [unnamed-chunk-2] (rada_vignette.Rmd) Error: processing vignette 'rada_vignette.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘rada_vignette.Rmd’
--- re-building ‘rada_vignette_supplemental.Rmd’ using knitr ... Quitting from lines at lines 62-70 [unnamed-chunk-2] (rada_vignette_supplemental.Rmd) Error: processing vignette 'rada_vignette_supplemental.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘rada_vignette_supplemental.Rmd’
SUMMARY: processing the following files failed: ‘rada_vignette.Rmd’ ‘rada_vignette_supplemental.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "RadioGx")
for more info
checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 3.5Mb
checking data for non-ASCII characters ... NOTE
Note: found 52 marked UTF-8 strings
Run revdep_details(, "RandomForestsGLS")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘RandomForestsGLS_user_guide.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'RandomForestsGLS_user_guide.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RandomForestsGLS/new/RandomForestsGLS.Rcheck/vign_test/RandomForestsGLS/vignettes/RandomForestsGLS_user_guide.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RandomForestsGLS_user_guide.log for more info. --- failed re-building ‘RandomForestsGLS_user_guide.Rmd’
SUMMARY: processing the following file failed: ‘RandomForestsGLS_user_guide.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "RBesT")
for more info
checking installed package size ... NOTE
installed size is 108.0Mb
sub-directories of 1Mb or more:
libs 106.2Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "regsem")
for more info
checking whether package ‘regsem’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/regsem/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/regsem/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/regsem/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/regsem/new/regsem.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
libs 5.9Mb
Run revdep_details(, "reservr")
for more info
checking whether package ‘reservr’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/reservr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/reservr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/reservr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/reservr/new/reservr.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 16.8Mb
sub-directories of 1Mb or more:
R 1.5Mb
libs 14.8Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "RGCCA")
for more info
checking running R code from vignettes ... ``` ‘RGCCA.Rmd’ using ‘UTF-8’... failed WARNING Errors in running code in vignettes: when running code in ‘RGCCA.Rmd’ ... > plot(fit.mcoa, type = "biplot", block = 4, comp = 1:2,
knitr::opts_chunk$set(eval = "gliomaData" %in% rownames(installed.packages()))
data("ge_cgh_locIGR", package = "gliomaData")
When sourcing ‘RGCCA.R’: Error: there is no package called ‘gliomaData’ Execution halted ```
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘RGCCA.Rmd’ using rmarkdown ! Package pgfkeys Error: I do not know the key '/tikz/orcidlogo/.pic' and I am going to ignore it. Perhaps you misspelled it.
Error: processing vignette 'RGCCA.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RGCCA/new/RGCCA.Rcheck/vign_test/RGCCA/vignettes/RGCCA.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RGCCA.log for more info. --- failed re-building ‘RGCCA.Rmd’
SUMMARY: processing the following file failed: ‘RGCCA.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "RiboDiPA")
for more info
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 2.9Mb
doc 1.3Mb
libs 1.3Mb
Run revdep_details(, "RJcluster")
for more info
checking whether package ‘RJcluster’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/RJcluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/RJcluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/RJcluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/RJcluster/new/RJcluster.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
libs 6.9Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘RJclust_Vignette.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'RJclust_Vignette.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RJcluster/new/RJcluster.Rcheck/vign_test/RJcluster/vignettes/RJclust_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RJclust_Vignette.log for more info. --- failed re-building ‘RJclust_Vignette.Rmd’
SUMMARY: processing the following file failed: ‘RJclust_Vignette.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "RNAmodR")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/55485c326a2c_2549' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/545cd44bb50_2537' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/545c59376ca5_2541' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/545c6bdc006a_2539' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/545c62013e41_2543' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/545c5837b49b_2545' ...
[ FAIL 1 | WARN 21 | SKIP 0 | PASS 898 ] Error: Test failures Execution halted ```
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'Biostrings:::XString'
'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList'
'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine'
'S4Vectors:::make_zero_col_DataFrame'
'S4Vectors:::prepare_objects_to_bind'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.get_inosine_score'
Run revdep_details(, "RNAseqQC")
for more info
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 3.5Mb
doc 2.2Mb
Run revdep_details(, "RnBeads")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
'ff', 'fields', 'ggplot2', 'gplots', 'grid', 'gridExtra', 'limma',
'matrixStats', 'illuminaio', 'methylumi', 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
R 3.1Mb
doc 3.7Mb
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘qvalue’
A package should be listed in only one of these fields.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’
A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file. ```
checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'grid'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
‘stopCluster’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘varLabels’
...
plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable
refText reg.type region.size registerDoParallel relative.coord
removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs
seqlengths seqlevels<- setNames sigCategories sigset.l sites2ignore
size solve.QP stopCluster sva target texthere tsne type types
ucscTableQuery universeCounts useMart v var.diff varFit varLabels x
x2 xmlValue y y2 yint
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘RnBeads.Rnw’ using Sweave
Error: processing vignette 'RnBeads.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RnBeads.tex' failed.
LaTeX errors:
! LaTeX Error: File
vmargin.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty)
... l.10 \usepackage [english,american]{babel}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘RnBeads_Annotations.Rnw’
SUMMARY: processing the following files failed: ‘RnBeads.Rnw’ ‘RnBeads_Annotations.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "robustlm")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "rpm")
for more info
checking tests ... ``` Running ‘tests.R’ ERROR Running the tests in ‘tests/tests.R’ failed. Complete output: > > library(testthat) > library(rpm) Loading required package: abind Loading required package: future Loading required package: doRNG ...
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted ```
checking whether package ‘rpm’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/rpm/new/rpm.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 11.6Mb
sub-directories of 1Mb or more:
libs 11.1Mb
Run revdep_details(, "rsvddpd")
for more info
checking whether package ‘rsvddpd’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/rsvddpd/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/rsvddpd/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/rsvddpd/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/rsvddpd/new/rsvddpd.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
Run revdep_details(, "rtrend")
for more info
checking whether package ‘rtrend’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/rtrend/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/rtrend/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/rtrend/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/rtrend/new/rtrend.Rcheck/00install.out’ for details.
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
Run revdep_details(, "samr")
for more info
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Run revdep_details(, "SANvi")
for more info
checking whether package ‘SANvi’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/SANvi/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/SANvi/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/SANvi/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SANvi/new/SANvi.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
libs 9.1Mb
Run revdep_details(, "scDataviz")
for more info
installed size is 6.5Mb
sub-directories of 1Mb or more:
doc 5.7Mb
Run revdep_details(, "scDHA")
for more info
checking whether package ‘scDHA’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/scDHA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/scDHA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/scDHA/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/scDHA/new/scDHA.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
data 3.2Mb
libs 4.3Mb
Run revdep_details(, "scISR")
for more info
Namespace in Imports field not imported from: ‘markdown’
All declared Imports should be used.
Run revdep_details(, "scITD")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/scITD/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/scITD/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/scITD/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/scITD/new/scITD.Rcheck/00install.out’ for details.
Run revdep_details(, "scmap")
for more info
checking whether package ‘scmap’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/scmap/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/scmap/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/scmap/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/scmap/new/scmap.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 2.6Mb
doc 1.1Mb
libs 2.3Mb
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
All declared Imports should be used.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘scmap.Rmd’ using rmarkdown
Quitting from lines at lines 15-17 [knitr-options] (scmap.Rmd) Error: processing vignette 'scmap.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘scmap.Rmd’
SUMMARY: processing the following file failed: ‘scmap.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "scMET")
for more info
checking running R code from vignettes ... ``` ‘scMET_vignette.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘scMET_vignette.Rmd’ ...
library(knitr)
opts_chunk$set(error = FALSE, message = TRUE, warning = FALSE)
knitr::include_graphics("../inst/figures/scmet-motivation.png")
When sourcing ‘scMET_vignette.R’: Error: Cannot find the file(s): "../inst/figures/scmet-motivation.png" Execution halted ```
checking installed package size ... NOTE
installed size is 74.4Mb
sub-directories of 1Mb or more:
doc 3.4Mb
libs 69.7Mb
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_scmet” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_scmet” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "scone")
for more info
sconeReport: no visible global function definition for
‘visNetworkOutput’
sconeReport: no visible global function definition for ‘plotlyOutput’
sconeReport : server: no visible global function definition for
‘renderVisNetwork’
sconeReport : server: no visible global function definition for ‘%>%’
sconeReport : server: no visible global function definition for
‘visNetwork’
sconeReport : server: no visible global function definition for
‘visHierarchicalLayout’
...
sconeReport : server: no visible global function definition for
‘geom_point’
sconeReport : server: no visible global function definition for
‘guides’
Undefined global functions or variables:
%>% aes coord_cartesian element_blank geom_bar geom_point geom_violin
ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork
scale_fill_manual theme visEdges visGroups visHierarchicalLayout
visLegend visNetwork visNetworkOutput visNetworkProxy visOptions
visSelectNodes ylim
Run revdep_details(, "scp")
for more info
checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
doc 7.0Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MultiAssayExperiment:::.sampleMapFromData’ ‘QFeatures:::.get_Hits’
‘QFeatures:::.normIndex’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE
readSCPfromDIANN: no visible global function definition for
‘pivot_wider’
Undefined global functions or variables:
pivot_wider
Run revdep_details(, "scPCA")
for more info
Namespaces in Imports field not imported from:
‘DelayedArray’ ‘matrixStats’
All declared Imports should be used.
Run revdep_details(, "sctransform")
for more info
checking whether package ‘sctransform’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/sctransform/new/sctransform.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘glmGamPoi’
Run revdep_details(, "seagull")
for more info
checking whether package ‘seagull’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/seagull/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/seagull/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/seagull/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/seagull/new/seagull.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 12.1Mb
sub-directories of 1Mb or more:
libs 11.5Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘seagull.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'seagull.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/seagull/new/seagull.Rcheck/vign_test/seagull/vignettes/seagull.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See seagull.log for more info. --- failed re-building ‘seagull.Rmd’
SUMMARY: processing the following file failed: ‘seagull.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "sechm")
for more info
checking R code for possible problems ... NOTE
homogenizeDEA: no visible global function definition for ‘head’
homogenizeDEA: no visible global function definition for ‘p.adjust’
setRowAttr : <anonymous>: no visible global function definition for
‘setNames’
Undefined global functions or variables:
head p.adjust setNames
Consider adding
importFrom("stats", "p.adjust", "setNames")
importFrom("utils", "head")
to your NAMESPACE file.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘ggplot2’
Run revdep_details(, "sensobol")
for more info
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/sensobol/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/sensobol/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/sensobol/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/sensobol/new/sensobol.Rcheck/00install.out’ for details.
Run revdep_details(, "seqArchR")
for more info
checking examples ... ERROR ``` Running examples in ‘seqArchR-Ex.R’ failed The error most likely occurred in:
Name: seqArchR
Title: seqArchR: A package for de novo discovery of different sequence
architectures
Aliases: seqArchR
** Examples
...
── Outer chunk 1 of 1 [Size: 200] ──
── Inner chunk 1 of 2 [Size: 100] Error: BiocParallel errors 2 remote errors, element index: 1, 51 98 unevaluated and other errors first remote error: Error: Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 4. └─seqArchR (local) FUN(X[[i]], ...) 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) ... 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...)
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ] Error: Test failures Execution halted ```
Run revdep_details(, "Seurat")
for more info
checking package dependencies ... NOTE
Packages suggested but not available for checking: 'BPCells', 'presto'
checking installed package size ... NOTE
installed size is 16.0Mb
sub-directories of 1Mb or more:
R 1.7Mb
libs 13.5Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘Signac’
Run revdep_details(, "SGP")
for more info
checking running R code from vignettes ... ``` ‘SGP.Rmd’... failed ‘SGP_Data_Analysis.Rmd’... failed ‘SGP_Data_Preparation.Rmd’... failed ERROR Errors in running code in vignettes: when running code in ‘SGP.Rmd’ ... > knitr::opts_chunk$set(collapse = TRUE, comment = "",
...
knitr::opts_chunk$set(collapse = TRUE, comment = "", + prompt = TRUE, fig.dpi = 96)
if (is_html_output()) { + options(width = 1000) + }
When sourcing ‘SGP_Data_Preparation.R’: Error: argument is of length zero Execution halted ```
checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
R 1.3Mb
doc 3.8Mb
Run revdep_details(, "SIAMCAT")
for more info
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 23.4Mb
sub-directories of 1Mb or more:
doc 18.4Mb
extdata 2.1Mb
help 1.9Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘ranger’
Run revdep_details(, "SICtools")
for more info
checking whether package ‘SICtools’ can be installed ... WARNING
Found the following significant warnings:
bam.c:128:2: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
bam_index.c:178:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow]
razf.c:178:2: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SICtools/new/SICtools.Rcheck/00install.out’ for details.
checking examples ... WARNING ``` Found the following significant warnings:
Warning: 'applyPileups' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Rsamtools', 'doParallel', 'Biostrings', 'stringr', 'matrixStats',
'plyr', 'GenomicRanges', 'IRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE
.indelDiffFunc: no visible global function definition for ‘fisher.test’
.indelDiffFunc: no visible global function definition for ‘dist’
indelDiff: no visible global function definition for ‘read.delim’
snpDiff : calcInfoRange : <anonymous>: no visible global function
definition for ‘fisher.test’
snpDiff : calcInfoRange : <anonymous>: no visible global function
definition for ‘dist’
Undefined global functions or variables:
dist fisher.test read.delim
Consider adding
importFrom("stats", "dist", "fisher.test")
importFrom("utils", "read.delim")
to your NAMESPACE file.
Run revdep_details(, "sigminer")
for more info
installed size is 5.9Mb
sub-directories of 1Mb or more:
help 1.7Mb
libs 1.4Mb
Run revdep_details(, "SimBu")
for more info
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
.pre-commit-config.yaml
.prettierignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking whether package ‘SimBu’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SimBu/new/SimBu.Rcheck/00install.out’ for details.
Run revdep_details(, "simona")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 25.3Mb
sub-directories of 1Mb or more:
doc 10.4Mb
libs 13.2Mb
Run revdep_details(, "simPop")
for more info
checking whether package ‘simPop’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/simPop/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/simPop/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/simPop/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/simPop/new/simPop.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 5.0Mb
Run revdep_details(, "sindyr")
for more info
Namespaces in Imports field not imported from:
‘crqa’ ‘plot3D’
All declared Imports should be used.
Run revdep_details(, "Single.mTEC.Transcriptomes")
for more info
checking running R code from vignettes ... ``` ‘mTECs.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘mTECs.Rnw’ ...
write.table(dfPrint, quote = FALSE, sep = "\t", row.names = FALSE, + file = "figure/tspan8CoexpressionGroup.txt") Warning in file(file, ifelse(append, "a", "w")) : cannot open file 'figure/tspan8CoexpressionGroup.txt': No such file or directory
When sourcing ‘mTECs.R’: Error: cannot open the connection Execution halted ```
checking installed package size ... NOTE
installed size is 904.4Mb
sub-directories of 1Mb or more:
data 895.1Mb
doc 9.3Mb
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘mTECs.Rnw’ using knitr The magick package is required to crop "figure/Figure_1C_variableNoMarker-1.png" but not available. The magick package is required to crop "figure/Figure_1A_trasvsgenes-1.png" but not available. The magick package is required to crop "figure/Figure_Supp1_percentageTRAs-1.png" but not available. The magick package is required to crop "figure/Figure_1B_saturation-1.png" but not available. The magick package is required to crop "figure/Figure_Supp2_traenrichment-1.png" but not available. The magick package is required to crop "figure/Figure_1D1_histogramAire-1.png" but not available. The magick package is required to crop "figure/Figure_1D2_histogramAire-1.png" but not available. The magick package is required to crop "figure/Figure_1D3_histogramAire-1.png" but not available. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘mTECs.Rnw’
SUMMARY: processing the following file failed: ‘mTECs.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "singscore")
for more info
plotDispersion: no visible binding for global variable ‘Score’
plotDispersion: no visible binding for global variable ‘Dispersion’
plotDispersion: no visible binding for global variable ‘Class’
plotDispersion: no visible binding for global variable ‘SampleText’
plotDispersion: no visible binding for global variable ‘SampleLabel’
plotRankDensity_intl: no visible binding for global variable ‘Ranks’
plotRankDensity_intl: no visible binding for global variable ‘upDown’
plotRankDensity_intl: no visible binding for global variable
‘..density..’
plotRankDensity_intl: no visible binding for global variable ‘EntrezID’
...
plotScoreLandscape: no visible binding for global variable ‘sc1’
plotScoreLandscape: no visible binding for global variable ‘sc2’
projectScoreLandscape: no visible binding for global variable
‘SampleText’
projectScoreLandscape: no visible binding for global variable ‘Class’
projectScoreLandscape: no visible binding for global variable
‘SampleLabel’
Undefined global functions or variables:
..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText
Score sc1 sc2 upDown
Run revdep_details(, "SkeweDF")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "slasso")
for more info
checking whether package ‘slasso’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/slasso/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/slasso/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/slasso/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/slasso/new/slasso.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RcppArmadillo’
All declared Imports should be used.
Run revdep_details(, "sparrow")
for more info
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.1Mb
doc 2.0Mb
extdata 2.1Mb
checking R code for possible problems ... NOTE
geneSetsStats: no visible binding for global variable ‘direction’
Undefined global functions or variables:
direction
Run revdep_details(, "SparseArray")
for more info
checking compiled code ... NOTE ``` File ‘SparseArray/libs/SparseArray.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "sparseMatrixStats")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 4.9Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘SummarizedExperiment’
Run revdep_details(, "spathial")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘irlba’ ‘knitr’ ‘rmarkdown’
All declared Imports should be used.
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "spatzie")
for more info
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
Run revdep_details(, "SpliceWiz")
for more info
checking examples ... ERROR ``` Running examples in ‘SpliceWiz-Ex.R’ failed The error most likely occurred in:
Name: getAvailableGO
Title: Builds reference files used by SpliceWiz
Aliases: getAvailableGO Build-Reference-methods getResources buildRef
buildFullRef getNonPolyARef
** Examples
... ...CDS ...exons done Apr 10 10:19:52 AM Retrieving gene GO-term pairings Warning: Couldn't set synchronous mode: database disk image is malformed Use
synchronous
= NULL to turn off this warning. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘removeResources’ for signature ‘"AnnotationHub"’ Calls: buildRef ... .check_cached_resource -> removeResources -> Execution halted ```
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking installed package size ... NOTE
installed size is 18.5Mb
sub-directories of 1Mb or more:
R 2.2Mb
doc 4.9Mb
libs 10.3Mb
Run revdep_details(, "splitFeas")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘corpcor’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "spqn")
for more info
Package in Depends field not imported from: ‘BiocGenerics’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Run revdep_details(, "stabiliser")
for more info
Namespace in Imports field not imported from: ‘knitr’
All declared Imports should be used.
Run revdep_details(, "stapler")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "stm")
for more info
checking whether package ‘stm’ can be installed ... WARNING
Found the following significant warnings:
/c4/home/henrik/repositories/matrixStats/revdep/library/stm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/stm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
/c4/home/henrik/repositories/matrixStats/revdep/library/stm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/stm/new/stm.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 1.7Mb
libs 3.2Mb
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘stmVignette.Rnw’ using Sweave
stm v1.3.7 successfully loaded. See ?stm for help.
Papers, resources, and other materials at structuraltopicmodel.com
Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'stmVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File
ulem.sty' not found.
... l.57 ^^M
! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'stmVignette.Rnw'
SUMMARY: processing the following file failed: 'stmVignette.Rnw'
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "STROMA4")
for more info
checking examples ... ERROR ``` Running examples in ‘STROMA4-Ex.R’ failed The error most likely occurred in:
Name: assign.properties
Title: Function to assign properties to an expression matrix
Aliases: assign.properties
** Examples
library(breastCancerMAINZ) ... + genelists=c('Stroma4', 'TNBCType'), n=10) --Assigning properties to expression data-- --There are duplicated genes. Using most variable to collapse-- ----206 out of 297 total genes matching for D.stroma.property---- Error: BiocParallel errors 10 remote errors, element index: 1, 2, 3, 4, 5, 6, ... 0 unevaluated and other errors first remote error: Error: [matrixStats] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of matrixStats. This is because the current default ties.method="max" will eventually be updated to ties.method="average" in order to align with the default of base::rank() Execution halted ```
checking running R code from vignettes ... ``` ‘STROMA4-vignette.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘STROMA4-vignette.Rnw’ ...
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") Installing package into ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/STROMA4/new/STROMA4.Rcheck’ (as ‘lib’ is unspecified)
When sourcing ‘STROMA4-vignette.R’: Error: trying to use CRAN without setting a mirror Execution halted ```
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘BiocManager’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘STROMA4-vignette.Rnw’ using Sweave Installing package into ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/STROMA4/new/STROMA4.Rcheck’ (as ‘lib’ is unspecified)
Error: processing vignette 'STROMA4-vignette.Rnw' failed with diagnostics: chunk 1 Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror
--- failed re-building ‘STROMA4-vignette.Rnw’
SUMMARY: processing the following file failed: ‘STROMA4-vignette.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "summarytools")
for more info
checking whether package ‘summarytools’ can be installed ... WARNING
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/summarytools/new/summarytools.Rcheck/00install.out’ for details.
checking data for non-ASCII characters ... NOTE
Note: found 78 marked UTF-8 strings
Run revdep_details(, "susieR")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘finemapping.Rmd’ using rmarkdown --- finished re-building ‘finemapping.Rmd’
--- re-building ‘finemapping_summary_statistics.Rmd’ using rmarkdown --- finished re-building ‘finemapping_summary_statistics.Rmd’
--- re-building ‘mwe.Rmd’ using rmarkdown --- finished re-building ‘mwe.Rmd’
... l.8 \usepackage {xspace}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘trendfiltering_derivations.Rnw’
SUMMARY: processing the following file failed: ‘trendfiltering_derivations.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "sva")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘sva.Rnw’ using Sweave Loading required package: mgcv Loading required package: nlme This is mgcv 1.9-1. For overview type 'help("mgcv-package")'. Loading required package: genefilter Loading required package: BiocParallel Loading required package: Biobase Loading required package: BiocGenerics
... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘sva.Rnw’
SUMMARY: processing the following file failed: ‘sva.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "TCA")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Matrix’ ‘quadprog’
All declared Imports should be used.
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "templateICAr")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE
installed size is 17.0Mb
sub-directories of 1Mb or more:
libs 16.6Mb
Run revdep_details(, "topGO")
for more info
checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi',
'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking startup messages can be suppressed ... NOTE ```
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘Rgraphviz’ ‘multtest’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘globaltest:::globaltest’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘topGO.Rnw’ using Sweave
Loading required package: xtable Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
... l.11 \usepackage {caption}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘topGO.Rnw’
SUMMARY: processing the following file failed: ‘topGO.Rnw’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "tradeSeq")
for more info
checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
doc 6.4Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Biobase’ ‘igraph’
All declared Imports should be used.
checking R code for possible problems ... NOTE
.earlyDETest: no visible binding for global variable ‘X1’
.earlyDETest: no visible binding for global variable ‘X2’
.findKnots: no visible binding for global variable ‘t1’
.findKnots: no visible binding for global variable ‘l1’
.plotGeneCount: no visible binding for global variable ‘dim1’
.plotGeneCount: no visible binding for global variable ‘dim2’
.plotSmoothers: no visible binding for global variable ‘time’
.plotSmoothers: no visible binding for global variable ‘gene_count’
.plotSmoothers: no visible binding for global variable ‘lineage’
.plotSmoothers_conditions: no visible binding for global variable
...
‘pCol’
.plotSmoothers_sce: no visible binding for global variable ‘time’
.plotSmoothers_sce: no visible binding for global variable ‘gene_count’
.plotSmoothers_sce: no visible binding for global variable ‘lineage’
.plotSmoothers_sce: no visible binding for global variable ‘pCol’
Undefined global functions or variables:
X1 X2 dim1 dim2 gene_count l1 lineage pCol t1 time
Consider adding
importFrom("stats", "time")
to your NAMESPACE file.
Run revdep_details(, "TRESS")
for more info
checkRd: (-1) CallCandidates.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) CallCandidates.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.multiRep.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.paramEsti.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.paramEsti.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) findBumps.Rd:8: Escaped LaTeX specials: \&
Run revdep_details(, "VanillaICE")
for more info
checking Rd files ... WARNING
checkRd: (5) VanillaICE.Rd:0-7: Must have a \description
checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'doMC', 'doMPI', 'doSNOW', 'doParallel', 'doRedis'
checking startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BSgenome.Hsapiens.UCSC.hg18’ ‘MatrixGenerics’
All declared Imports should be used.
Run revdep_details(, "variancePartition")
for more info
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘FAQ.Rmd’ using rmarkdown --- finished re-building ‘FAQ.Rmd’
--- re-building ‘additional_visualization.Rmd’ using rmarkdown --- finished re-building ‘additional_visualization.Rmd’
--- re-building ‘dream.Rmd’ using rmarkdown
Quitting from lines at lines 145-161 [lmm] (dream.Rmd) ... --- finished re-building ‘rnd_effects.Rmd’
--- re-building ‘variancePartition.Rmd’ using rmarkdown --- finished re-building ‘variancePartition.Rmd’
SUMMARY: processing the following file failed: ‘dream.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
data 1.3Mb
doc 5.7Mb
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘lmerTest:::as_lmerModLT’
See the note in ?`:::` about the use of this operator.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'residuals.MArrayLM2': ‘residuals.MArrayLM2’
The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
‘GSEABase’ ‘doParallel’
Run revdep_details(, "VaSP")
for more info
checking running R code from vignettes ... ``` ‘VaSP.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘VaSP.Rmd’ ...
options(tinytex.verbose = TRUE)
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
knitr::include_graphics("../README_files/VaSP.png")
When sourcing ‘VaSP.R’: Error: Cannot find the file(s): "../README_files/VaSP.png" Execution halted ```
checking installed package size ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
doc 3.6Mb
extdata 3.4Mb
Run revdep_details(, "Voyager")
for more info
checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 50 lines of output:
Error in `loadNamespace(x)`: there is no package called 'DropletUtils'
Backtrace:
▆
1. ├─SpatialFeatureExperiment::read10xVisiumSFE(".", images = "lowres") at test-plot.R:925:1
2. │ └─base::lapply(...)
3. │ └─SpatialFeatureExperiment (local) FUN(X[[i]], ...)
...
• plot/plotcorrelogram-coldata-i.svg
• plot/plotcorrelogram-continuous-color-by.svg
• plot/plotcorrelogram-one-gene-c.svg
• plot/plotcorrelogram-one-gene-corr.svg
• plot/plotcorrelogram-specify-gene-and-coldata-i.svg
• plot/plotdimloadings-not-balanced.svg
• plot/with-subset-freqpoly.svg
• plot/with-subset.svg
Error: Test failures
Execution halted
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'variogram-internal.Rd': ‘variogram’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
doc 5.1Mb
Run revdep_details(, "vsclust")
for more info
checking for code/documentation mismatches ... WARNING ``` Codoc mismatches from documentation object 'estimClustNum': estimClustNum Code: function(dat, maxClust = 25, scaling = "standardize", cores = 1) Docs: function(dat, maxClust = 25, cores = 1) Argument names in code not in docs: scaling Mismatches in argument names: Position: 3 Code: scaling Docs: cores
... runClustWrapper Code: function(dat, NClust, proteins = NULL, VSClust = TRUE, scaling = "standardize", cores, verbose = FALSE) Docs: function(dat, NClust, proteins = NULL, VSClust = TRUE, cores, verbose = FALSE) Argument names in code not in docs: scaling Mismatches in argument names: Position: 5 Code: scaling Docs: cores Position: 6 Code: cores Docs: verbose ```
checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
doc 4.4Mb
libs 1.7Mb
checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE
runFuncEnrich: no visible global function definition for
‘compareCluster’
runFuncEnrich: no visible global function definition for ‘new’
Undefined global functions or variables:
compareCluster new
Consider adding
importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking Rd files ... NOTE
prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso
prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples
Run revdep_details(, "WaverideR")
for more info
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/WaverideR/new/WaverideR.Rcheck/00install.out’ for details.
Run revdep_details(, "WeMix")
for more info
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/WeMix/new/WeMix.Rcheck/vign_test/WeMix/vignettes/Introduction_to_Mixed_Effects_Models_With_WeMix.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction_to_Mixed_Effects_Models_With_WeMix.log for more info. --- failed re-building ‘Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd’ ... Error: processing vignette 'Weighted_Linear_Mixed_Effects_Models.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/WeMix/new/WeMix.Rcheck/vign_test/WeMix/vignettes/Weighted_Linear_Mixed_Effects_Models.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Weighted_Linear_Mixed_Effects_Models.log for more info. --- failed re-building ‘Weighted_Linear_Mixed_Effects_Models.Rmd’
SUMMARY: processing the following files failed: ‘Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd’ ‘Weighted_Linear_Mixed_Effects_Models.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "WGCNA")
for more info
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'empiricalBayesLM.Rd': ‘rlm’
See section 'Cross-references' in the 'Writing R Extensions' manual. ```
Run revdep_details(, "yarn")
for more info
checking examples ... ERROR ``` Running examples in ‘yarn-Ex.R’ failed The error most likely occurred in:
Name: annotateFromBiomart
Title: Annotate your Expression Set with biomaRt
Aliases: annotateFromBiomart
** Examples
...
subsetting and changing column name just for a silly example
skin <- skin[1:10,] colnames(fData(skin)) = paste("names",1:6) biomart<-"ENSEMBL_MART_ENSEMBL"; genes <- sapply(strsplit(rownames(skin),split="\."),function(i)i[1]) newskin <-annotateFromBiomart(skin,genes=genes,biomar=biomart) Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. Calls: annotateFromBiomart -> useMart -> .useMart -> useDataset -> checkDataset Execution halted ```
checking re-building of vignette outputs ... NOTE
``
Error(s) in re-building vignettes:
...
--- re-building ‘yarn.Rmd’ using rmarkdown
! LaTeX Error: File
iftex.sty' not found.
! Emergency stop.
Error: processing vignette 'yarn.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/yarn/new/yarn.Rcheck/vign_test/yarn/vignettes/yarn.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See yarn.log for more info. --- failed re-building ‘yarn.Rmd’
SUMMARY: processing the following file failed: ‘yarn.Rmd’
Error: Vignette re-building failed. Execution halted ```
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