Version: 0.0.1
Namespaces in Imports field not imported from:
‘devtools’ ‘httr’
All declared Imports should be used.
Version: 0.7
Namespaces in Imports field not imported from:
‘fields’ ‘knitr’
All declared Imports should be used.
Version: 0.18-0
Packages unavailable to check Rd xrefs: ‘ez’, ‘ascii’
Version: 0.0.1
Namespaces in Imports field not imported from:
‘DBI’ ‘assertthat’ ‘tibble’
All declared Imports should be used.
Version: 0.5.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 58 SKIPPED: 0 FAILED: 9 1. Failure: .convert_time correctly parses string (@test_data.R#7) 2. Failure: .convert_time correctly parses string (@test_data.R#11) 3. Failure: .convert_time correctly parses string (@test_data.R#13) 4. Failure: .convert_time correctly parses string (@test_data.R#16) 5. Failure: .convert_time correctly parses string (@test_data.R#20) 6. Failure: .convert_time correctly parses string (@test_data.R#23) 7. Failure: .convert_time correctly parses string (@test_data.R#26) 8. Failure: .convert_time correctly parses string (@test_data.R#30) 9. Failure: .convert_time correctly parses string (@test_data.R#33)
Error: testthat unit tests failed Execution halted ```
checking data for non-ASCII characters ... NOTE
Note: found 38 marked UTF-8 strings
Version: 0.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > library(testthat) > library(alphavantager) > > test_check("alphavantager")
testthat results ================================================================ OK: 11 SKIPPED: 0 FAILED: 1 1. Error: call SECTOR (@test_av_get.R#38)
Error: testthat unit tests failed Execution halted ```
Namespace in Imports field not imported from: ‘devtools’
All declared Imports should be used.
Version: 0.2.8
installed size is 15.7Mb
sub-directories of 1Mb or more:
data 15.6Mb
Version: 1.3
Note: found 3597 marked UTF-8 strings
Version: 1.2.1
checking re-building of vignette outputs ... WARNING
...
Building 1to5kb upstream of TSS...
Building intergenic...
Building 5UTRs...
Building 3UTRs...
Building exons...
Building introns...
Building intron exon boundaries...
snapshotDate(): 2017-04-25
Building CpG islands...
loading from cache '/home/muelleki//.AnnotationHub/5086'
Building CpG shores...
Building CpG shelves...
Building inter-CpG-islands...
Annotating...
Randomizing regions...
`summarise_each()` is deprecated.
Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
To map `funs` over a selection of variables, use `summarise_at()`
Error: processing vignette 'annotatr-vignette.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
checking R code for possible problems ... NOTE
plot_coannotations: no visible binding for global variable ‘.’
plot_numerical_coannotations: no visible binding for global variable
‘.’
Undefined global functions or variables:
.
Version: 0.2.4
Namespace in Imports field not imported from: ‘caret’
All declared Imports should be used.
Version: 2.1.2
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘archivist.github’
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘rmarkdown’, ‘archivist.github’
Version: 0.0-3
Package unavailable to check Rd xrefs: ‘pryr’
Version: 2.0.2.2
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Actual value: "Unknown column
tree` "
tree
"testthat results ================================================================ OK: 374 SKIPPED: 0 FAILED: 2 1. Failure: assert breaks appropriately (@test-assertions.R#232) 2. Failure: assert_rows breaks appropriately (@test-assertions.R#334)
Error: testthat unit tests failed Execution halted ```
Version: 1.0.0
Namespace in Imports field not imported from: ‘tidyr’
All declared Imports should be used.
Version: 0.1.6
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: > library(testthat) > test_check("backtestGraphics") Loading required package: backtestGraphics
truth.1
.
Component "pnl": Component "pnl.drawdown": Component "start": Attributes: < Component "levels": 1 string mismatch >
Component "pnl": Component "pnl.drawdown": Component "start": 1 string mismatchtestthat results ================================================================ OK: 9 SKIPPED: 0 FAILED: 1 1. Failure: stat_calculation function (@test_stat_calculation.R#8)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.0
Namespaces in Imports field not imported from:
‘XML’ ‘devtools’ ‘ggplot2’ ‘scales’
All declared Imports should be used.
Version: 0.2.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 6 SKIPPED: 0 FAILED: 1 1. Error: Geocode tbl works (@test_geocodetbl.R#16)
Error: testthat unit tests failed Execution halted ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘stringr’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 1.4.0
installed size is 5.8Mb
sub-directories of 1Mb or more:
R 1.6Mb
doc 3.6Mb
Version: 0.1.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 660 marked UTF-8 strings
Version: 1.8.0
Found the following significant warnings:
Warning: replacing previous import ‘dplyr::exprs’ by ‘Biobase::exprs’ when loading ‘biobroom’
See ‘/home/muelleki/git/R/dplyr/revdep/checks/biobroom/new/biobroom.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE
'library' or 'require' call to ‘DESeq2’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: ‘dplyr::tbl_dt’
checking R code for possible problems ... NOTE
...
for ‘colData’
tidy.deSet: no visible global function definition for ‘exprs<-’
tidy.deSet: no visible binding for global variable ‘value’
tidy.deSet: no visible binding for global variable ‘gene’
tidy.deSet: no visible global function definition for ‘pData’
tidy.qvalue: no visible binding for global variable ‘smoothed’
tidy.qvalue: no visible binding for global variable ‘pi0’
tidy.qvalue: no visible binding for global variable ‘lambda’
tidy_matrix: no visible binding for global variable ‘value’
tidy_matrix: no visible binding for global variable ‘gene’
Undefined global functions or variables:
. DGEList calcNormFactors colData counts design end estimate
estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix
p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames
setNames smoothed start tbl_dt term value voom voomWithQualityWeights
Consider adding
importFrom("methods", "is")
importFrom("stats", "end", "model.matrix", "p.adjust", "setNames",
"start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Version: 1.4.0
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Error: processing vignette 'bioCancer.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘magrittr’ ‘ggplot2’ ‘lubridate’ ‘tidyr’ ‘cgdsr’ ‘RCurl’ ‘XML’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 22.3Mb
sub-directories of 1Mb or more:
base 6.9Mb
bioCancer 3.1Mb
doc 2.8Mb
quant 7.7Mb
Version: 1.0.1
...
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Auto-disconnecting SQLiteConnection
Error: processing vignette 'BiocFileCache.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
Version: 0.5.2
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: download_url, "' currently available?", call. = FALSE)
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt' Content type 'unknown' length 2921997 bytes (2.8 MB) ================================================== trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/assembly_summary.txt' Content type 'unknown' length 362999 bytes (354 KB) ================================================== testthat results ================================================================ OK: 40 SKIPPED: 0 FAILED: 1 1. Error: The getAssemblyStats() downloads assembly stats file and reads raw input: NCBI Genbank .. (@test-getAssemblyStats.R#34)
Error: testthat unit tests failed Execution halted ```
Version: 1.0.4
Namespaces in Imports field not imported from:
‘Matrix’ ‘SuperLearner’ ‘biotmleData’
All declared Imports should be used.
Version: 1.0
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘bigrf’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
‘rmarkdown’ ‘shinyjs’
All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Version: 1.3.3
checking installed package size ... NOTE
installed size is 32.9Mb
sub-directories of 1Mb or more:
libs 32.6Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Version: 0.1
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 8.7Mb
Version: 0.0.8
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [2055] "IDE00437.201711152040.tif" "IDE00437.201711152050.tif" [2057] "IDE00437.201711152100.tif" "IDE00437.201711152110.tif" [2059] "IDE00437.201711152120.tif" "IDE00437.201711152130.tif" [2061] "IDE00437.201711152140.tif" "IDE00437.201711152150.tif"
testthat results ================================================================ OK: 102 SKIPPED: 0 FAILED: 2 1. Error: caching utils list files in cache and delete when asked (@test-check_cache.R#47) 2. Error: get_available_imagery functions properly (@test-get_satellite_imagery.R#21)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.0
Namespaces in Imports field not imported from:
‘rgdal’ ‘tidyr’
All declared Imports should be used.
Version: 0.1.0
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 6.1Mb
Version: 0.1.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘sp’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘ggthemes’
Version: 0.4.0
checking tests ...
``
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
12: map_mold(.x, .f, logical(1), ...)
13: vapply(.x, .f, .mold, ..., USE.NAMES = FALSE)
14: df[keep_cols]
15:
[.tbl_df`(df, keep_cols)
16: check_names_df(i, x)
17: check_names_df.default(i, x)
18: stopc("Unsupported index type: ", class(j)[[1L]])
19: abort(paste0(...))
testthat results ================================================================ OK: 359 SKIPPED: 0 FAILED: 1 1. Error: Columns without names are renamed (@test_cleanup_data.R#72)
Error: testthat unit tests failed Execution halted ```
Package unavailable to check Rd xrefs: ‘breathteststan’
Version: 0.4.0
installed size is 28.9Mb
sub-directories of 1Mb or more:
libs 28.7Mb
Version: 0.4.2
checking examples ... ERROR ``` ...
colnames<-
(*tmp*
, value = c("conf.low", "conf.high")) :
attempt to set 'colnames' on an object with less than two dimensions
Calls: tidy -> tidy.gmm -> process_lm -> colnames<-
Execution halted
```checking tests ...
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("broom")
Loading required package: broom
Error in lahman_df() : could not find function "lahman_df"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> tbl
testthat results ================================================================
OK: 621 SKIPPED: 0 FAILED: 0
Execution halted
Version: 1.1.2
Namespaces in Imports field not imported from:
‘rworldxtra’ ‘sp’
All declared Imports should be used.
Version: 2.6.0
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning in get_engine(options$engine) :
Unknown language engine 'rr' (must be registered via knit_engines$set()).
Warning in get_engine(options$engine) :
Unknown language engine 'rr' (must be registered via knit_engines$set()).
Warning in get_engine(options$engine) :
Unknown language engine 'rr' (must be registered via knit_engines$set()).
Error: processing vignette 'BubbleTree-vignette.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
checking installed package size ... NOTE
installed size is 25.4Mb
sub-directories of 1Mb or more:
data 22.9Mb
doc 2.2Mb
checking R code for possible problems ... NOTE
annoByOverlap,Annotate: no visible binding for global variable
'queryHits'
Undefined global functions or variables:
queryHits
Version: 0.2.2
Namespace in Imports field not imported from: ‘markdown’
All declared Imports should be used.
Version: 1.17.4
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 0.2.1
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Retrieving tables from http://opendata.cbs.nl/ODataCatalog/Tables?$format=json&$filter=(Language%20eq%20'en') Quitting from lines 29-34 (cbsodata.Rmd) Error: processing vignette 'cbsodata.Rmd' failed with diagnostics: Required package curl not found. Please run: install.packages('curl') Execution halted ```
Version: 0.7.0
Installation failed.
See ‘/home/muelleki/git/R/dplyr/revdep/checks/cdcfluview/new/cdcfluview.Rcheck/00install.out’ for details.
* installing *source* package ‘cdcfluview’ ...
** package ‘cdcfluview’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
Error in seq.int(0, to0 - from, by) : 'to' must be a finite number
Error : unable to load R code in package ‘cdcfluview’
ERROR: lazy loading failed for package ‘cdcfluview’
* removing ‘/home/muelleki/git/R/dplyr/revdep/checks/cdcfluview/new/cdcfluview.Rcheck/cdcfluview’
* installing *source* package ‘cdcfluview’ ...
** package ‘cdcfluview’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
Error in seq.int(0, to0 - from, by) : 'to' must be a finite number
Error : unable to load R code in package ‘cdcfluview’
ERROR: lazy loading failed for package ‘cdcfluview’
* removing ‘/home/muelleki/git/R/dplyr/revdep/checks/cdcfluview/old/cdcfluview.Rcheck/cdcfluview’
Version: 1.0.0
checking Rd \usage sections ... WARNING ``` Duplicated \argument entries in documentation object 'dfs_tree': ‘chrom_bounds’ ‘ncols’ ‘chrom_bounds’ ‘cnv_data’ ‘chrom_bounds’ ‘n_bp_per_pixel’ ‘mut_data’ ‘width’ ‘height’ ‘mutations’ ‘height’ ‘width’ ‘clonal_prev’ ‘tree_edges’ ‘alpha’ ‘clonal_prev’ ‘tree_edges’ ‘genotype_position’ ‘clone_colours’ ‘perturbations’ ‘mutations’ ‘tree_edges’ ‘clonal_prev’ ‘clonal_prev’ ‘tree_edges’ ‘clone_colours’ ‘mutations’
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 re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 76-92 (cellscape_vignette.Rmd)
Error: processing vignette 'cellscape_vignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘plyr’
All declared Imports should be used.
checking R code for possible problems ... NOTE
...
getMutOrder: no visible binding for global variable ‘VAF’
getMutOrder: no visible global function definition for ‘lm’
getMutOrder: no visible binding for global variable ‘na.omit’
getMutOrder: no visible global function definition for ‘coef’
getMutationsData: no visible binding for global variable
‘show_warnings’
getTargetedHeatmapForEachSC: no visible binding for global variable
‘single_cell_id’
getTargetedHeatmapForEachSC: no visible binding for global variable
‘chr’
getTargetedHeatmapForEachSC: no visible binding for global variable
‘coord’
Undefined global functions or variables:
VAF chr chrom_index coef combn coord copy_number cumsum_values dist
genotype hclust lm melt mode_cnv n n_gt na.omit px px_width sc_id
setNames show_warnings single_cell_id site timepoint
Consider adding
importFrom("stats", "coef", "dist", "hclust", "lm", "na.omit",
"setNames")
importFrom("utils", "combn")
to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘devtools’
Version: 0.1.0
Note: found 287 marked UTF-8 strings
Version: 0.6.7
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘gamlss.dist’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 20 marked UTF-8 strings
Version: 1.12.1
checking re-building of vignette outputs ... WARNING ``` ... DOSE v3.2.0 For help: https://guangchuangyu.github.io/DOSE
If you use DOSE in published research, please cite: Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609
clusterProfiler v3.4.4 For help: https://guangchuangyu.github.io/clusterProfiler
If you use clusterProfiler in published research, please cite: Guangchuang Yu., Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. ReactomePA v1.20.2 For help: https://guangchuangyu.github.io/ReactomePA
If you use ReactomePA in published research, please cite: Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479 ChIPseeker v1.12.1 For help: https://guangchuangyu.github.io/ChIPseeker
If you use ChIPseeker in published research, please cite: Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383 'select()' returned 1:many mapping between keys and columns Error: processing vignette 'ChIPseeker.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
Version: 0.1
checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
na.omit
Consider adding
importFrom("stats", "na.omit")
to your NAMESPACE file.
Version: 1.4.0
checking re-building of vignette outputs ... WARNING ``` ...
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Warning: call dbDisconnect() when finished working with a connection Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'CINdex.tex' failed. LaTeX errors: ! LaTeX Error: File `biblatex.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty)
! Emergency stop.
l.76 \usepackage [english]{babel}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```
checking installed package size ... NOTE
installed size is 18.4Mb
sub-directories of 1Mb or more:
data 17.7Mb
checking R code for possible problems ... NOTE
comp.heatmap: no visible binding for global variable ‘dataMatrix’
process.probe.anno: no visible binding for global variable ‘ID’
process.probe.anno: no visible binding for global variable ‘midpoint’
process.reference.genome: no visible binding for global variable
‘chrom’
process.reference.genome: no visible binding for global variable ‘name’
process.reference.genome: no visible binding for global variable
‘stain’
Undefined global functions or variables:
ID chrom dataMatrix midpoint name stain
Version: 0.8.0
checking package dependencies ... ERROR ``` Package required but not available: ‘rzmq’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 0.1.0
Namespace in Imports field not imported from: ‘tidyr’
All declared Imports should be used.
Version: 1.6.1
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'labelSwitching':
labelSwitching
Code: function(object, ...)
Docs: function(object, merge = TRUE)
Argument names in code not in docs:
...
Argument names in docs not in code:
merge
Mismatches in argument names:
Position: 2 Code: ... Docs: merge
checking installed package size ... NOTE
installed size is 12.7Mb
sub-directories of 1Mb or more:
libs 10.6Mb
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicRanges’
A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE
consensusRegion: no visible global function definition for
‘elementLengths’
Undefined global functions or variables:
elementLengths
Version: 0.3.1
Error in re-building vignettes:
...
Quitting from lines 478-486 (codingMatrices.Rnw)
Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics:
xtable not installed.
Execution halted
Version: 1.10.0
checking whether package ‘cogena’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
Warning: replacing previous import ‘dplyr::exprs’ by ‘Biobase::exprs’ when loading ‘cogena’
See ‘/home/muelleki/git/R/dplyr/revdep/checks/cogena/new/cogena.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
doc 1.9Mb
extdata 3.1Mb
checking R code for possible problems ... NOTE
...
corInCluster,cogena: no visible global function definition for ‘cor’
heatmapCluster,cogena: no visible global function definition for
‘topo.colors’
heatmapCluster,cogena: no visible global function definition for
‘rainbow’
heatmapCluster,cogena: no visible global function definition for ‘par’
heatmapCluster,cogena: no visible global function definition for
‘legend’
Undefined global functions or variables:
abline as.dist axis cor data density dist hist image layout legend
lines median mtext order.dendrogram p.adjust par phyper plot.new
rainbow rect reorder sd text title topo.colors
Consider adding
importFrom("grDevices", "rainbow", "topo.colors")
importFrom("graphics", "abline", "axis", "hist", "image", "layout",
"legend", "lines", "mtext", "par", "plot.new", "rect",
"text", "title")
importFrom("stats", "as.dist", "cor", "density", "dist", "median",
"order.dendrogram", "p.adjust", "phyper", "reorder", "sd")
importFrom("utils", "data")
to your NAMESPACE file.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘clValid’
Version: 0.1.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 0.1.6
Packages which this enhances but not available for checking:
‘knitr’ ‘shiny’
Version: 0.1.0
Error in re-building vignettes:
...
Quitting from lines 93-97 (comtradr-vignette.Rmd)
Error: processing vignette 'comtradr-vignette.Rmd' failed with diagnostics:
too few arguments
Execution halted
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 51 SKIPPED: 0 FAILED: 1 1. Error: correct api vals given: 1 reporter, 2 partners, all trade directions, annual, only shrimp (@test-ct_search.R#51)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.1
Note: found 1 marked UTF-8 string
Version: 0.1.0
checking re-building of vignette outputs ... WARNING ``` ... The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
stat_bin()
using bins = 30
. Pick better value with binwidth
.
To use this package, you must install the hurricaneexposuredata
package. To install that package, run
install.packages('hurricaneexposuredata',
repos='https://geanders.github.io/drat/', type='source')
. See the
hurricaneexposure
vignette for more details.
To use this function, you must have the hurricaneexposuredata
package installed. See the hurricaneexposure
package vignette
for more details.
Quitting from lines 311-313 (countyflood.Rmd)
Error: processing vignette 'countyflood.Rmd' failed with diagnostics:
there is no package called 'hurricaneexposuredata'
Execution halted
```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘maps’
All declared Imports should be used.
Version: 0.1.0
Note: found 1 marked UTF-8 string
Version: 1.0.0
Note: found 11 marked Latin-1 strings
Note: found 57 marked UTF-8 strings
Version: 2.1.1
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 6.5Mb
Version: 0.1.1
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 1.2.0
checking re-building of vignette outputs ... WARNING ``` ...
html_document, md_document, pdf_document
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Using tags as id variables Using tags as id variables Using tags as id variables Using tags as id variables Error: processing vignette 'ctsGE.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
Version: 1.2.2
checking re-building of vignette outputs ... WARNING ``` ... The data you have provided does not have any singletons. This is highly suspicious. Results of richness estimates (for example) are probably unreliable, or wrong, if you have already trimmed low-abundance taxa from the data.
We recommended that you find the un-trimmed data and retry. Warning in graphics:::plotHclust(n1, merge, height, order(x$order), hang, : "method" is not a graphical parameter Warning in graphics:::plotHclust(n1, merge, height, order(x$order), hang, : "method" is not a graphical parameter Warning in axis(2, at = pretty(range(height)), ...) : "method" is not a graphical parameter Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Error: processing vignette 'curatedMetagenomicData.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘dplyr’ ‘phyloseq’ ‘Biobase’ ‘ExperimentHub’ ‘AnnotationHub’
‘magrittr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking installed package size ... NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
help 7.9Mb
checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocInstaller’
A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocInstaller’
All declared Imports should be used.
checking R code for possible problems ... NOTE
ExpressionSet2MRexperiment: no visible global function definition for
‘AnnotatedDataFrame’
ExpressionSet2MRexperiment: no visible global function definition for
‘phenoData’
curatedMetagenomicData : <anonymous>: no visible global function
definition for ‘exprs<-’
Undefined global functions or variables:
AnnotatedDataFrame exprs<- phenoData
checking Rd files ... NOTE
prepare_Rd: HMP_2012.Rd:540-542: Dropping empty section \seealso
prepare_Rd: KarlssonFH_2013.Rd:90-92: Dropping empty section \seealso
prepare_Rd: LeChatelierE_2013.Rd:86-88: Dropping empty section \seealso
prepare_Rd: LomanNJ_2013_Hi.Rd:82-84: Dropping empty section \seealso
prepare_Rd: LomanNJ_2013_Mi.Rd:82-84: Dropping empty section \seealso
prepare_Rd: NielsenHB_2014.Rd:94-96: Dropping empty section \seealso
prepare_Rd: Obregon_TitoAJ_2015.Rd:94-96: Dropping empty section \seealso
prepare_Rd: OhJ_2014.Rd:86-88: Dropping empty section \seealso
prepare_Rd: QinJ_2012.Rd:106-108: Dropping empty section \seealso
prepare_Rd: QinN_2014.Rd:94-96: Dropping empty section \seealso
prepare_Rd: RampelliS_2015.Rd:90-92: Dropping empty section \seealso
prepare_Rd: TettAJ_2016.Rd:184-186: Dropping empty section \seealso
prepare_Rd: ZellerG_2014.Rd:94-96: Dropping empty section \seealso
Version: 0.7.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Failed with error: 'there is no package called 'V8''
testthat results ================================================================ OK: 11 SKIPPED: 3 FAILED: 2 1. Error: d3-jetpack on latest release (@test_deps.R#47) 2. Error: d3_v8 has d3 (@test_v8.R#9)
Error: testthat unit tests failed Execution halted ```
checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
‘igraph’ ‘partykit’ ‘treemap’ ‘V8’
Version: 0.2.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 0.3.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tests/testthat/test-summarise.r:963:1: style: lines should not be more than 100 characters. expect_identical(summarise(group_by(mtcars, cyl), x = n(), z = x)[2:3], tibble(x = c(11L, 7L, 14L), z = x)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tests/testthat/test-summarise.r:987:1: style: lines should not be more than 100 characters. expect_error(summarise(gdf, out = !! 1:5), "must be length 2 (the number of groups)", fixed = TRUE) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
testthat results ================================================================ OK: 108 SKIPPED: 0 FAILED: 1 1. Failure: Package Style (@test-lintr.R#5)
Error: testthat unit tests failed Execution halted ```
Version: 0.8.6
Package suggested but not available for checking: ‘Rhipe’
Version: 2.7.3
Version: 0.4.0
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 78-85 (Introduction_to_datasus.Rmd) Error: processing vignette 'Introduction_to_datasus.Rmd' failed with diagnostics: Timeout was reached: Connection timed out after 10000 milliseconds Execution halted ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RCurl’
All declared Imports should be used.
Version: 1.1.0
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
Version: 1.2.10
deepblue_enrich_region_overlap(
Version: 1.12.0
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 R code for possible problems ... NOTE
...
‘plotCounts’
degPlotWide: no visible binding for global variable ‘gene’
degPlotWide: no visible binding for global variable ‘count’
degPlotWide: no visible binding for global variable ‘treatment’
degResults: no visible global function definition for ‘assay’
degResults: no visible global function definition for ‘rlog’
degResults: no visible global function definition for ‘results’
degResults: no visible global function definition for ‘colData’
degResults: no visible global function definition for ‘rowMax’
degVolcano: no visible binding for global variable ‘logFC’
degVolcano: no visible binding for global variable ‘V1’
degVolcano: no visible binding for global variable ‘V2’
degVolcano: no visible binding for global variable ‘adj.P.Val’
degVolcano: no visible binding for global variable ‘x’
degVolcano: no visible binding for global variable ‘y’
degVolcano: no visible binding for global variable ‘name’
Undefined global functions or variables:
MulticoreParam V1 V2 adj.P.Val assay bplapply coda.samples colData
comp count enrichGO gene group jags.model keys label log2FoldChange
logFC name one plotCounts results rlog rowMax simplify treatment two
value variable x y
Version: 1.2.5
checking S3 generic/method consistency ... WARNING ``` filter: function(x, filter, method, sides, circular, init) filter.cells: function(dl, .filter, number, cells)
filter: function(x, filter, method, sides, circular, init) filter.genes: function(dl, .filter, number, genes)
See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ```
Version: 2.0.2
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.4Mb
Version: 0.2.0
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tests/testthat/test-ts.R:8:1: style: lines should not be more than 80 characters.
"
.datamust be a data source, not a ts object, do you want
stats::filter()?",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tests/testthat/test-window.R:63:1: style: lines should not be more than 80 characters.
expect_error(order_by(NULL, !! 1L), "
call` must be a function call, not an integer vector")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
testthat results ================================================================ OK: 7 SKIPPED: 0 FAILED: 1 1. Failure: Package Style (@test-styling.R#4)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.0
checking examples ... ERROR ``` ...
With grouping on a factor
iris %>%
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'desctable'
The following object is masked from 'package:DT':
datatable
The following objects are masked from 'package:stats':
IQR, chisq.test, fisher.test
Quitting from lines 217-222 (desctable.Rmd) Error: processing vignette 'desctable.Rmd' failed with diagnostics: object 'Species' not found Execution halted ```
Version: 0.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ======================================================================================================================================================================================== OK: 54 SKIPPED: 0 FAILED: 4 1. Failure: myrpois works (@test-myrs.R#7) 2. Failure: best_tau works (@test_best_tau.R#7) 3. Failure: detrending works (@test_detrend.R#19) 4. Failure: detrending works (@test_detrend.R#29)
Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
extdata 2.4Mb
libs 4.1Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Version: 0.5.1
Note: found 109 marked UTF-8 strings
Version: 2.0.1
installed size is 27.5Mb
sub-directories of 1Mb or more:
doc 1.9Mb
libs 25.2Mb
Version: 2.4.8
checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
‘rgl’ ‘XLConnect’
checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
libs 3.3Mb
checking R code for possible problems ... NOTE
pv.DBAplotVolcano: no visible binding for global variable ‘Fold’
pv.DBAplotVolcano: no visible binding for global variable ‘Legend’
Undefined global functions or variables:
Fold Legend
Version: 1.4.0
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.
Version: 0.3.0
Package unavailable to check Rd xrefs: ‘arm’
Version: 1.11.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 1.1
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 4.9Mb
doc 1.2Mb
Version: 0.1.1
.gdf : find_loss: no visible global function definition for ‘rnorm’
.p.values : <anonymous>: no visible global function definition for
‘pnorm’
.relist.dwt: no visible global function definition for ‘relist’
.relist.dwt: no visible global function definition for ‘as’
.std.wav.coeff : <anonymous>: no visible global function definition for
‘mad’
regrid: no visible global function definition for ‘predict’
regrid: no visible global function definition for ‘var’
regrid: no visible global function definition for ‘medpolish’
Undefined global functions or variables:
as mad medpolish pnorm predict relist rnorm var
Consider adding
importFrom("methods", "as")
importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm",
"var")
importFrom("utils", "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Version: 2.2.8
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 2.2.1
checking installed package size ... NOTE
installed size is 73.6Mb
sub-directories of 1Mb or more:
data 23.9Mb
doc 1.5Mb
extdata 48.0Mb
checking R code for possible problems ... NOTE
...
‘biosample_type’
step6_control: no visible binding for global variable ‘controls’
step6_date_released: no visible binding for global variable
‘date_released’
step6_status: no visible binding for global variable ‘status’
step6_target: no visible binding for global variable ‘target’
step7: no visible binding for global variable ‘organism’
step8: no visible binding for global variable ‘investigated_as’
step8: no visible binding for global variable ‘target’
step9: no visible binding for global variable ‘organism’
Undefined global functions or variables:
. Experiment Value accession antibody_caption
antibody_characterization antibody_target assay
biological_replicate_number biosample_name biosample_type col_name
controls data date_released download.file encode_df file_accession
file_format href investigated_as lab nucleic_acid_term organism
platform project replicate_antibody replicate_library server status
submitted_by target technical_replicate_number treatment ui value
Consider adding
importFrom("utils", "data", "download.file")
to your NAMESPACE file.
checking data for non-ASCII characters ... NOTE
Note: found 771 marked UTF-8 strings
Version: 1.0.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 146 SKIPPED: 0 FAILED: 14
Error: testthat unit tests failed Execution halted ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘colorspace’
All declared Imports should be used.
Version: 0.1.2
Namespaces in Imports field not imported from:
‘magrittr’ ‘readr’
All declared Imports should be used.
Version: 0.4.0
Package unavailable to check Rd xrefs: ‘metafor’
Version: 0.1.0
Namespaces in Imports field not imported from:
‘ggalt’ ‘pander’ ‘psych’
All declared Imports should be used.
Missing or unexported object: ‘purrr::by_row’
Version: 0.34
checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
doc 5.8Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘curl’ ‘openxlsx’ ‘stringr’
All declared Imports should be used.
Version: 0.2.1
checking installed package size ... NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
exiftool 12.3Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 0.1.6
checking examples ... ERROR ``` ...
mutate_each()
is deprecated.
Use mutate_all()
, mutate_at()
or mutate_if()
instead.
To map funs
over a selection of variables, use mutate_at()
response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000,
response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate",
time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM",
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Computing t.test for each time bin...
Computing t.test for each time bin...
`mutate_each()` is deprecated.
Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead.
To map `funs` over a selection of variables, use `mutate_at()`
Avg. window length in new data will be 5500
Performing Trackloss Analysis...
Will exclude trials whose trackloss proportion is greater than : 0.25
...removed 33 trials.
Error in UseMethod("make_time_cluster_data") :
no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
Calls: test_check ... source_file -> eval -> eval -> make_time_cluster_data
testthat results ================================================================
OK: 38 SKIPPED: 0 FAILED: 0
Execution halted
Version: 0.2.0
installed size is 7.4Mb
sub-directories of 1Mb or more:
data 4.8Mb
libs 2.4Mb
Version: 0.2.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 1.6.0
checking re-building of vignette outputs ... WARNING
...
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'filehash'
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'filehash'
Preclustering resulted in 3326 gene groups (1.367 seconds elapsed)
Grouping resulted in 3140 gene groups (12.369 seconds elapsed)
Total time elapsed was 13.76 seconds
Presplitting resulted in 3161 gene groups (0.091 seconds elapsed)
Adding missing grouping variables: `org`, `contig`
Splitting resulted in 3602 gene groups (3 minutes and 23.428 seconds elapsed)
Adding missing grouping variables: `org`, `contig`
Adding missing grouping variables: `org`, `contig`
Adding missing grouping variables: `org`, `contig`
Adding missing grouping variables: `org`, `contig`
Adding missing grouping variables: `org`, `contig`
Adding missing grouping variables: `org`, `contig`
Merging resulted in 3414 gene groups (3.44 seconds elapsed)
Total time elapsed was 3 minutes and 26.959 seconds
Error: processing vignette 'FindMyFriends_intro.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
checking installed package size ... NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
extdata 1.8Mb
libs 5.6Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘gtable:::insert.unit’ ‘gtable:::z_arrange_gtables’
See the note in ?`:::` about the use of this operator.
Version: 0.1.3
Error in re-building vignettes:
...
pandoc: Could not find data file /usr/share/pandoc/data/templates/--highlight-style.html
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 97
Execution halted
Version: 0.3.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 6: pmap_chr(x, function(image_src, width, height) { format(external_img(src = image_src, width = width, height = height), type = type) }) 7: .f(image_src = .l[[c(1L, i)]], width = .l[[c(2L, i)]], height = .l[[c(3L, i)]], ...) 8: format(external_img(src = image_src, width = width, height = height), type = type) 9: external_img(src = image_src, width = width, height = height) 10: stopifnot(file.exists(src)) 11: stop(msg, call. = FALSE, domain = NA)
testthat results ================================================================ OK: 67 SKIPPED: 0 FAILED: 1 1. Error: images (@test-images.R#44)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: officer
Quitting from lines 323-336 (format.Rmd)
Error: processing vignette 'format.Rmd' failed with diagnostics:
file.exists(src) is not TRUE
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 3.24.4
checking if this is a source package ... NOTE
...
src/pb_build/src/google/protobuf/io/zero_copy_stream_impl_lite.lo
src/pb_build/src/google/protobuf/message.lo
src/pb_build/src/google/protobuf/message_lite.lo
src/pb_build/src/google/protobuf/reflection_ops.lo
src/pb_build/src/google/protobuf/repeated_field.lo
src/pb_build/src/google/protobuf/service.lo
src/pb_build/src/google/protobuf/stubs/atomicops_internals_x86_gcc.lo
src/pb_build/src/google/protobuf/stubs/atomicops_internals_x86_msvc.lo
src/pb_build/src/google/protobuf/stubs/common.lo
src/pb_build/src/google/protobuf/stubs/once.lo
src/pb_build/src/google/protobuf/stubs/stringprintf.lo
src/pb_build/src/google/protobuf/stubs/structurally_valid.lo
src/pb_build/src/google/protobuf/stubs/strutil.lo
src/pb_build/src/google/protobuf/stubs/substitute.lo
src/pb_build/src/google/protobuf/text_format.lo
src/pb_build/src/google/protobuf/unknown_field_set.lo
src/pb_build/src/google/protobuf/wire_format.lo
src/pb_build/src/google/protobuf/wire_format_lite.lo
src/pb_build/src/libprotobuf.la
src/protobuf-2.6.0/src/solaris/libstdc++.la
Object files/libraries should not be included in a source package.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
src/pb_build/src/google/protobuf/.dirstamp
src/pb_build/src/google/protobuf/io/.dirstamp
src/pb_build/src/google/protobuf/stubs/.dirstamp
src/pb_build/src/.libs
src/pb_build/src/google/protobuf/.libs
src/pb_build/src/google/protobuf/io/.libs
src/pb_build/src/google/protobuf/stubs/.libs
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 108.0Mb
sub-directories of 1Mb or more:
doc 1.1Mb
include 2.7Mb
lib 72.9Mb
libs 30.6Mb
checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘RSVGTipsDevice’ ‘parallel’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘RBGL’ ‘graphics’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘Rgraphviz:::getRenderPar’ ‘flowCore:::.estimateLogicle’
‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
‘flowCore:::logicle_transform’ ‘graph:::.makeEdgeKeys’
‘lattice:::updateList’ ‘ncdfFlow:::.isValidSamples’
‘stats:::.splinefun’
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_gs’ ‘.preprocessMap’ ‘.uuid_gen’ ‘isNegated’
checking R code for possible problems ... NOTE
...
rbind2,GatingSetList-missing: no visible global function definition for
‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
‘slot’
recompute,GatingSetList: no visible global function definition for
‘selectMethod’
transform,GatingSet: no visible global function definition for ‘is’
Undefined global functions or variables:
. .hasSlot IQR as as.formula callNextMethod decade dev.off dev.prev
dev.set extends gray groupName is max_val median min_val new node
offset old openCyto.count polygon rect sampleName selectMethod slot
strheight strwidth symbols text validObject xml.count
Consider adding
importFrom("grDevices", "dev.off", "dev.prev", "dev.set", "gray")
importFrom("graphics", "polygon", "rect", "strheight", "strwidth",
"symbols", "text")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "slot", "validObject")
importFrom("stats", "IQR", "as.formula", "median", "offset")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Version: 0.4.4
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 49 SKIPPED: 0 FAILED: 10
Error: testthat unit tests failed Execution halted ```
Version: 0.2.2
installed size is 5.0Mb
sub-directories of 1Mb or more:
libs 4.5Mb
Version: 1.0.4
Package unavailable to check Rd xrefs: ‘Hmisc’
Version: 0.1.6
checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘dggrids’ ```
checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 4.8Mb
doc 1.6Mb
Version: 0.8.17
Packages unavailable to check Rd xrefs: ‘alr3’, ‘doBy’, ‘psych’, ‘prettyR’, ‘fBasics’, ‘RMark’, ‘asbio’, ‘PMCMR’, ‘pgirmess’, ‘agricolae’, ‘DescTools’
Version: 0.1.8
installed size is 11.1Mb
sub-directories of 1Mb or more:
doc 2.2Mb
libs 8.7Mb
Version: 1.0
Note: found 39 marked UTF-8 strings
Version: 1.4.0
checking package dependencies ... ERROR ``` Package required but not available: ‘EBImage’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.0.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 129 SKIPPED: 0 FAILED: 15
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ...
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Error: processing vignette 'GA4GHclient.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
Version: 2.1-1
Namespace in Imports field not imported from: ‘scales’
All declared Imports should be used.
Version: 0.0.2
Namespaces in Imports field not imported from:
‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
All declared Imports should be used.
Version: 0.4.01
installed size is 58.6Mb
sub-directories of 1Mb or more:
libs 58.2Mb
Version: 1.0.3
Namespace in Imports field not imported from: ‘rootSolve’
All declared Imports should be used.
Version: 0.5.1
Package suggested but not available for checking: ‘genderdata’
Version: 1.2.0
checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
data 5.8Mb
checking R code for possible problems ... NOTE
...
barChart : geneXtender: no visible binding for global variable ‘type’
barChart : geneXtender: no visible binding for global variable ‘seqid’
barChart : geneXtender: no visible binding for global variable
‘gene_id’
barChart : geneXtender: no visible binding for global variable
‘gene_name’
distinct : geneXtender: no visible binding for global variable ‘type’
distinct : geneXtender: no visible binding for global variable ‘seqid’
distinct : geneXtender: no visible binding for global variable
‘gene_id’
distinct : geneXtender: no visible binding for global variable
‘gene_name’
linePlot : geneXtender: no visible binding for global variable ‘type’
linePlot : geneXtender: no visible binding for global variable ‘seqid’
linePlot : geneXtender: no visible binding for global variable
‘gene_id’
linePlot : geneXtender: no visible binding for global variable
‘gene_name’
peaksInput: no visible binding for global variable ‘chr’
Undefined global functions or variables:
chr gene_id gene_name seqid type
Version: 1.10.0
installed size is 11.0Mb
sub-directories of 1Mb or more:
doc 2.0Mb
extdata 7.9Mb
Version: 1.5.5
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
StartTag: invalid element name Extra content at the end of the document testthat results ================================================================ OK: 174 SKIPPED: 0 FAILED: 7 1. Error: download works (@test-download_result.R#8) 2. Error: load result works (@test-download_result.R#14) 3. Error: load result works from job id URL (@test-download_result.R#19) 4. Error: download result works from job id URL (@test-download_result.R#24) 5. Error: download result works from job (@test-download_result.R#29) 6. Failure: error on url (@test-geoknife_utils.R#15) 7. Error: you can set booleans as pass through (@test-webprocess_input.R#56)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 360-364 (geoknife.Rmd)
Error: processing vignette 'geoknife.Rmd' failed with diagnostics:
need finite 'xlim' values
Execution halted
Version: 1.36.0
checking re-building of vignette outputs ... WARNING ``` ...
The following objects are masked from 'package:Biobase':
combine, exprs
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 273-277 (GEOmetadb.Rmd) Error: processing vignette 'GEOmetadb.Rmd' failed with diagnostics: Condition message must be a string Execution halted ```
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 R code for possible problems ... NOTE
getSQLiteFile: no visible global function definition for
‘download.file’
Undefined global functions or variables:
download.file
Consider adding
importFrom("utils", "download.file")
to your NAMESPACE file.
Version: 0.1.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 3 SKIPPED: 0 FAILED: 2 1. Error: query returns a list of data.frames (@test_query.R#4) 2. Error: no problems if no results (@test_query.R#26)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 34-37 (geoparser.Rmd)
Error: processing vignette 'geoparser.Rmd' failed with diagnostics:
HTTP failure: 401
Execution halted
Version: 1.0
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/dplyr/revdep/checks/geotoolsR/new/geotoolsR.Rcheck/00install.out’ for details.
Version: 1.2
Namespaces in Imports field not imported from:
‘DT’ ‘shinydashboard’
All declared Imports should be used.
Version: 1.8.0
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'c,Phenotypes-method':
\S4method{c}{Phenotypes}
Code: function(x, ...)
Docs: function(x, ..., recursive = FALSE)
Argument names in docs not in code:
recursive
checking R code for possible problems ... NOTE
.gespeR.cv: no visible global function definition for ‘coef’
.select.model: no visible global function definition for ‘predict’
concordance: no visible global function definition for ‘cor’
lasso.rand: no visible global function definition for ‘runif’
plot.gespeR: no visible global function definition for ‘hist’
stability.selection: no visible global function definition for ‘lm’
Phenotypes,character: no visible global function definition for
‘read.delim’
Undefined global functions or variables:
coef cor hist lm predict read.delim runif
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "coef", "cor", "lm", "predict", "runif")
importFrom("utils", "read.delim")
to your NAMESPACE file.
Version: 0.1.10
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 6: .stopAsciiWriting(x) 7: raster(x@file@name) 8: raster(x@file@name) 9: .local(x, ...) 10: .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", ...) 11: .rasterFromASCIIFile(x, ...) 12: stop("\"NROWS\" not detected")
testthat results ================================================================ OK: 107 SKIPPED: 0 FAILED: 2 1. Failure: cache directory is created if necessary (@test_caching.R#30) 2. Error: caching utils list files in cache and delete when asked (@test_caching.R#46)
Error: testthat unit tests failed Execution halted ```
Version: 0.8
checking examples ... ERROR ``` Running examples in ‘GetLattesData-Ex.R’ failed The error most likely occurred in:
Name: gld_get_lattes_data
Title: Downloads and reads Lattes data based on a vector of Lattes ids
Aliases: gld_get_lattes_data
** Examples
l.out <- gld_get_lattes_data(id.vec = 'K4713546D3', + field.qualis = 'ECONOMIA')
Downloading file /home/muelleki/tmp/Rtmp5NXsJR/K4713546D3_2017-11-16.zipWarning in utils::download.file(url = my.link, destfile = dest.file, quiet = T, : unable to resolve 'buscacv.cnpq.br' Error in utils::download.file(url = my.link, destfile = dest.file, quiet = T, : cannot open URL 'http://buscacv.cnpq.br/buscacv/rest/download/curriculo/K4713546D3' Calls: gld_get_lattes_data -> sapply -> lapply -> FUN -> Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4: identical(as.vector(object), TRUE) 5: as.vector(object) 6: gld_get_lattes_data("K4713546D3", folder.dl = "lattes files") 7: sapply(X = id.vec, FUN = gld_download_lattes_files, folder.dl = folder.dl) 8: lapply(X = X, FUN = FUN, ...) 9: FUN(X[[i]], ...) 10: utils::download.file(url = my.link, destfile = dest.file, quiet = T, mode = "wb", method = "internal")
testthat results ================================================================ OK: 1 SKIPPED: 0 FAILED: 1 1. Error: Test of main function (@test_gld.R#5)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 36-45 (gld_vignette-ReadLattes.Rmd)
Error: processing vignette 'gld_vignette-ReadLattes.Rmd' failed with diagnostics:
cannot open URL 'http://buscacv.cnpq.br/buscacv/rest/download/curriculo/K4713546D3'
Execution halted
Version: 0.4.0
Namespace in Imports field not imported from: ‘plotly’
All declared Imports should be used.
Version: 0.1.0
checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 6.1Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggmap’ ‘gridExtra’ ‘scales’ ‘tnet’
All declared Imports should be used.
Version: 0.1
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
Version: 0.3.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 2356 marked UTF-8 strings
Version: 0.1.0
Namespaces in Imports field not imported from:
‘colorspace’ ‘grid’
All declared Imports should be used.
Version: 0.4.1
checking examples ... ERROR ``` Running examples in ‘ggfortify-Ex.R’ failed The error most likely occurred in:
Name: gglagplot
Title: Plot time series against lagged versions of themselves
Aliases: gglagplot
** Examples
gglagplot(AirPassengers) Error:
x
must be a vector, not a ts object, do you wantstats::lag()
? Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: expect_equal(class(res$max_g) , c("POSIXct", "POSIXt")) ~^
testthat results ================================================================ OK: 1616 SKIPPED: 0 FAILED: 6 1. Failure: autoplot.aareg works for lung (@test-surv.R#220) 2. Failure: autoplot.aareg works for lung (@test-surv.R#221) 3. Failure: autoplot.aareg works for lung (@test-surv.R#222) 4. Failure: autoplot.aareg works for lung (@test-surv.R#223) 5. Error: gglagplot (@test-tslib.R#103) 6. Failure: Code Lint (@test_lint.R#27)
Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 5.0Mb
Version: 0.1.1
Namespaces in Imports field not imported from:
‘gridExtra’ ‘lazyeval’ ‘readr’
All declared Imports should be used.
Version: 0.1.3
Namespace in Imports field not imported from: ‘knitr’
All declared Imports should be used.
Version: 0.1.2
Namespaces in Imports field not imported from:
‘NHANES’ ‘gridExtra’
All declared Imports should be used.
Version: 0.1.3
Namespaces in Imports field not imported from:
‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
All declared Imports should be used.
Version: 0.1.6
Package unavailable to check Rd xrefs: ‘FactoMineR’
Version: 2.0.1
Namespace in Imports field not imported from: ‘randomForest’
All declared Imports should be used.
Version: 1.0.0
checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 3.0Mb
libs 2.8Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > > if (Sys.getenv("NOT_CRAN") == "true") { # like global skip_on_cran
Initial plotError in file(filename, "r", encoding = encoding) : cannot open the connection Calls: test_check ... source -> withVisible -> eval -> eval -> source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file '../../inst/ggraptR/functions/helper.R': No such file or directory testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
All declared Imports should be used.
Version: 0.4.3
Package unavailable to check Rd xrefs: ‘plyr’
Version: 0.4.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 4 SKIPPED: 0 FAILED: 19
Error: testthat unit tests failed Execution halted ```
Version: 0.2.2
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(googlesheets) > > if (identical(tolower(Sys.getenv("NOT_CRAN")), "true")) {
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 37-41 (basic-usage.Rmd)
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
Cannot read token from alleged .rds file:
../tests/testthat/googlesheets_token.rds
Execution halted
Version: 1.8.0
checking whether the package can be unloaded cleanly ... WARNING
Error: package or namespace load failed for ‘gQTLstats’:
.onLoad failed in loadNamespace() for 'Homo.sapiens', details:
call: loadMethod(structure(function (object)
error: could not find function "loadMethod"
Execution halted
checking whether the namespace can be loaded with stated dependencies ... WARNING ``` Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted
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 S3 generic/method consistency ... WARNING
...
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checking replacement functions ... WARNING
...
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
checking for code/documentation mismatches ... WARNING
...
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc
Execution halted
checking installed package size ... NOTE
installed size is 65.8Mb
sub-directories of 1Mb or more:
data 11.0Mb
doc 1.1Mb
registries 18.9Mb
vcf 33.8Mb
checking dependencies in R code ... NOTE
...
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc
Execution halted
checking foreign function calls ... NOTE
...
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking R code for possible problems ... NOTE
Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details:
call: loadMethod(structure(function (object)
error: could not find function "loadMethod"
Execution halted
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘MultiAssayExperiment’
checking Rd \usage sections ... NOTE
...
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc
Execution halted
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 data for non-ASCII characters ... NOTE
Note: found 8 marked Latin-1 strings
Note: found 12 marked UTF-8 strings
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘org.Hs.eg.db’
Version: 1.6.5
checking package dependencies ... ERROR ``` Package required but not available: ‘hexSticker’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.0.0
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘GRASP2’ ‘checkAnti’ ‘getJoinCompatible’
Undocumented data sets:
‘mml10p_nox’ ‘uniqueGexNames2.0’ ‘uniquePPDnames2.0’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking data for non-ASCII characters ... WARNING
Warning: found non-ASCII string
'Beh<e7>et's disease' in object 'uniquePPDnames2.0'
checking data for ASCII and uncompressed saves ... WARNING ```
Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress mml10p_nox.rda 7.1Mb 2.8Mb xz uniquePPDnames2.0.rda 17Kb 15Kb bzip2 ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 15-16 (BiocGRASP2.Rmd)
Error: processing vignette 'BiocGRASP2.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘AnnotationHubData’
checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 7.1Mb
checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Artistic-2.0 + file LICENSE
checking R code for possible problems ... NOTE
.grasp2ToAnnotationHub: no visible global function definition for
‘outputFile’
checkAnti: no visible binding for global variable ‘chr_hg19’
getJoinCompatible: no visible binding for global variable ‘gwrngs19’
Undefined global functions or variables:
chr_hg19 gwrngs19 outputFile
checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
Version: 1.5.2.4
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘taxstats’
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Version: 1.2
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘rmeta’
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'printCrudeAndAdjustedModel': ‘rbind.printCrudeAndAdjusted’ ‘cbind.printCrudeAndAdjusted’
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. ```
Version: 1.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: skip = skip, comment = comment, n_max = n_max, guess_max = guess_max, progress = progress) 4: read_connection(file) 5: open(con, "rb") 6: open.connection(con, "rb")
testthat results ================================================================ OK: 50 SKIPPED: 0 FAILED: 4 1. Error: .download_files properly works, subsetting for country and agroclimatology works and .process_gz returns a data table (@test-process_gz.R#23) 2. Error: reformat_GSOD file_list parameter reformats data properly (@test-reformat_GSOD.R#15) 3. Error: Timeout options are reset on update_station_list() exit (@test-update_station_list.R#6) 4. Error: update_station_list() downloads and imports proper file (@test-update_station_list.R#13)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.3
Note: found 13617 marked UTF-8 strings
Version: 0.2.2
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
Version: 0.1
checking examples ... ERROR ``` Running examples in ‘hdr-Ex.R’ failed The error most likely occurred in:
Name: get_data
Title: Fetch data from the UNDP Human Development Report
Aliases: get_data
** Examples
Get the Human Development Index for Germany in 2013
df <- get_data(indicator = 137506, country = "DEU", year = 2013) Error in curl::curl_fetch_memory(url, handle = handle) : Failed to connect to ec2-52-1-168-42.compute-1.amazonaws.com port 80: Connection refused Calls: get_data ... request_fetch -> request_fetch.write_memory -> -> .Call Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 31-33 (undp_hdr.Rmd)
Error: processing vignette 'undp_hdr.Rmd' failed with diagnostics:
Failed to connect to ec2-52-1-168-42.compute-1.amazonaws.com port 80: Connection refused
Execution halted
Version: 1.11.1
checking R code for possible problems ... NOTE
...
makeChunks: no visible global function definition for ‘breakInChunks’
makeChunks: no visible global function definition for ‘detectCores’
makeChunks : <anonymous>: no visible global function definition for
‘keepSeqlevels’
makeChunks : <anonymous>: no visible global function definition for
‘seqlevelsInUse’
makeGRanges: no visible global function definition for ‘IRanges’
makeGRanges: no visible global function definition for ‘seqlengths’
makeGRanges: no visible global function definition for ‘seqlevels<-’
makeGRanges: no visible global function definition for ‘sortSeqlevels’
makeGRanges: no visible global function definition for ‘seqlevelsInUse’
makeGRanges: no visible global function definition for ‘seqlengths<-’
makeGRanges: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
IRanges breakInChunks countQueryHits detectCores dist featureName
keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths
seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels
subjectHits
Consider adding
importFrom("stats", "dist")
to your NAMESPACE file.
checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
Version: 0.5.0
installed size is 16.5Mb
sub-directories of 1Mb or more:
doc 13.7Mb
htmlwidgets 1.9Mb
Version: 1.12.0
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
...
‘qBaseInsert’
read.psl : <anonymous>: no visible binding for global variable
‘tBaseInsert’
read.psl: no visible binding for global variable ‘matches’
read.psl: no visible binding for global variable ‘misMatches’
read.psl: no visible binding for global variable ‘qBaseInsert’
read.psl: no visible binding for global variable ‘tBaseInsert’
read.sampleInfo: no visible global function definition for ‘SimpleList’
splitSeqsToFiles: no visible global function definition for
‘fasta.info’
vpairwiseAlignSeqs: no visible global function definition for ‘Rle’
vpairwiseAlignSeqs: no visible global function definition for
‘runLength’
vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’
vpairwiseAlignSeqs: no visible global function definition for
‘runValue’
Undefined global functions or variables:
DataFrame IRanges IRangesList Rle ScanBamParam SimpleList
breakInChunks clusteredValue clusteredValue.freq detectCores
fasta.info matches mclapply metadata metadata<- misMatches
qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert
Version: 1.0.0
names(iniloc) <- list('day','month','year','lat','lon') tag <- as.POSIXct(paste(iniloc[1,1], '/', iniloc[1,2], '/', iniloc[1,3], sep=''),
pop <- as.POSIXct(paste(iniloc[2,1], '/', iniloc[2,2], '/', iniloc[2,3], sep=''),
read and format the example data
tag.sst <- read.wc(ptt, sstFile, type = 'sst', tag=tag, pop=pop) Error in findDateFormat(data$Date) : No correct date format was found. Calls: read.wc ... as.POSIXlt -> as.POSIXlt.character -> strptime -> findDateFormat Execution halted ```
Version: 1.3.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Sparsity threshold: 0.3 Density window: 1.72-1.75 Sparsity threshold: 0.2 Density window: 1.72-1.75 Sparsity threshold with the most rejected hypotheses: 0 testthat results ================================================================ OK: 189 SKIPPED: 0 FAILED: 5
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
...
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
Quitting from lines 68-72 (beta_diversity_ordinations.Rmd)
Error: processing vignette 'beta_diversity_ordinations.Rmd' failed with diagnostics:
Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength'
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘igraph’
All declared Imports should be used.
Version: 0.0.1
Package suggested but not available for checking: ‘hurricaneexposuredata’
Version: 1.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message) 5: withVisible(code) 6: rmarkdown::render("table-tester-2.Rmd", quiet = TRUE, output_format = "pdf_document") 7: convert(output_file, run_citeproc) 8: pandoc_convert(utf8_input, pandoc_to, output_format$pandoc$from, output, citeproc, output_format$pandoc$args, !quiet) 9: stop("pandoc document conversion failed with error ", result, call. = FALSE)
testthat results ================================================================ OK: 289 SKIPPED: 48 FAILED: 2 1. Error: Row heights do not screw up LaTeX multicol (@test-with-pandoc.R#20) 2. Error: table-tester-2.Rmd renders without errors in LaTeX (@test-with-pandoc.R#27)
Error: testthat unit tests failed Execution halted ```
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘xtable’
Version: 0.5
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
epsg (SRID): NA
proj4string: +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +units=m +no_defs
Reading layer
NHDWaterbody_projected' from data source /home/muelleki/.local/share/hydrolinks/unzip/NHD_H_0709_Shape.zip/NHDWaterbody_projected.shp' using driver
ESRI Shapefile'
Simple feature collection with 11444 features and 15 fields
geometry type: POLYGON
dimension: XY
bbox: xmin: 440230.1 ymin: 2040969 xmax: 630976.5 ymax: 2330831
epsg (SRID): NA
proj4string: +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +units=m +no_defs
testthat results ================================================================
OK: 8 SKIPPED: 0 FAILED: 1
Error: testthat unit tests failed Execution halted ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘sp’
All declared Imports should be used.
Version: 0.1-2
...
Gscores: no visible global function definition for ‘filter’
MiniDscores: no visible global function definition for ‘filter’
MiniDscores: no visible global function definition for ‘object.size’
RobustScores: no visible global function definition for ‘filter’
SplitHalf: no visible global function definition for ‘cor’
TestRetest: no visible global function definition for ‘filter’
TestRetest: no visible global function definition for ‘cor’
WPRscores: no visible global function definition for ‘filter’
WPRscores: no visible global function definition for ‘quantile’
WPRscores: no visible global function definition for ‘sd’
computeMinid: no visible global function definition for ‘sd’
doP1P2: no visible global function definition for ‘filter’
doP1P2: no visible global function definition for ‘sd’
doP1P2P3P4: no visible global function definition for ‘filter’
specialvar: no visible global function definition for ‘var’
Undefined global functions or variables:
cor filter object.size quantile sd var
Consider adding
importFrom("stats", "cor", "filter", "quantile", "sd", "var")
importFrom("utils", "object.size")
to your NAMESPACE file.
Version: 1.0.0
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 R code for possible problems ... NOTE
ideal: no visible binding for '<<-' assignment to ‘ideal_env’
ideal : <anonymous>: no visible binding for global variable ‘airway’
ideal : <anonymous>: no visible binding for global variable ‘ideal_env’
Undefined global functions or variables:
airway ideal_env
Version: 0.1.2
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘MASS’ ‘Rdpack’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘shiny’, ‘bayesm’, ‘ChoiceModelR’, ‘RSGHB’
Version: 1.4.0
checking re-building of vignette outputs ... WARNING ``` ...
intersect, setdiff, setequal, union
estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing
Attaching package: 'ggplot2'
The following object is masked from 'package:IHW':
alpha
Warning: Removed 30633 rows containing missing values (geom_point). Warning: Removed 13044 rows containing missing values (geom_point). Error: processing vignette 'introduction_to_ihw.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE
...
ihw.default: no visible global function definition for ‘p.adjust’
ihw_convex: no visible global function definition for ‘gurobi’
ihw_internal: no visible global function definition for ‘p.adjust’
ihw_milp: no visible global function definition for ‘str’
ihw_milp: no visible global function definition for ‘gurobi’
plot_decisionboundary: no visible binding for global variable ‘stratum’
plot_decisionboundary: no visible binding for global variable
‘covariate’
plot_decisionboundary: no visible binding for global variable ‘pvalue’
plot_decisionboundary: no visible binding for global variable ‘fold’
thresholds_ihwResult: no visible global function definition for
‘na.exclude’
thresholds,ihwResult: no visible global function definition for
‘na.exclude’
Undefined global functions or variables:
covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude
p.adjust pvalue runif str stratum
Consider adding
importFrom("stats", "na.exclude", "p.adjust", "runif")
importFrom("utils", "str")
to your NAMESPACE file.
Version: 1.4.0
Found the following significant warnings:
Warning: replacing previous import ‘dplyr::exprs’ by ‘Biobase::exprs’ when loading ‘IHWpaper’
See ‘/home/muelleki/git/R/dplyr/revdep/checks/IHWpaper/new/IHWpaper.Rcheck/00install.out’ for details.
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Error: processing vignette 'BH-explanation.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
checking installed package size ... NOTE
installed size is 14.9Mb
sub-directories of 1Mb or more:
doc 3.4Mb
extdata 9.8Mb
checking R code for possible problems ... NOTE
scott_fdrreg: no visible global function definition for ‘FDRreg’
scott_fdrreg: no visible global function definition for ‘getFDR’
sim_fun_eval: no visible binding for global variable ‘fdr_method’
sim_fun_eval: no visible binding for global variable ‘fdr_pars’
sim_fun_eval: no visible binding for global variable ‘FDP’
sim_fun_eval: no visible binding for global variable ‘rj_ratio’
sim_fun_eval: no visible binding for global variable ‘FPR’
sim_fun_eval: no visible binding for global variable ‘FWER’
Undefined global functions or variables:
FDP FDRreg FPR FWER fdr_method fdr_pars getFDR rj_ratio
Version: 0.40.2
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘spatstat’
checking installed package size ... NOTE
installed size is 43.7Mb
sub-directories of 1Mb or more:
data 1.4Mb
doc 4.9Mb
extdata 1.0Mb
include 2.8Mb
libs 33.0Mb
Version: 0.1.4
checking examples ... ERROR ``` ... > ### Aliases: imf_ids > > ### ** Examples > > imf_ids()
Downloading: 860 B Downloading: 860 B Downloading: 860 B Downloading: 860 B Request failed [404]. Retrying in 1 seconds...
Downloading: 860 B Downloading: 860 B Downloading: 860 B Downloading: 860 B Request failed [404]. Retrying in 1.5 seconds...
Downloading: 860 B Downloading: 860 B Downloading: 860 B Downloading: 860 B Error: data.imf.org appears to be down. Execution halted ```
Version: 0.6.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("incadata")
messages
does not match "2 files downloaded to".
Actual value: "1 files downloaded to /home/muelleki/tmp/Rtmp6Gv7wK/doc\n"Using tempfile: /home/muelleki/tmp/Rtmp6Gv7wK/ex_data925d28731f65.csv2 [1] "ex_data925d28731f65.csv2" file size: 1103 kb testthat results ================================================================ OK: 49 SKIPPED: 0 FAILED: 1 1. Failure: documents (@test-find_register.R#32)
Error: testthat unit tests failed Execution halted ```
checking data for non-ASCII characters ... NOTE
Note: found 568 marked UTF-8 strings
Version: 1.0.1
Namespace in Imports field not imported from: ‘testthat’
All declared Imports should be used.
Version: 1.0.1
Namespaces in Imports field not imported from:
‘dplyr’ ‘rgeos’
All declared Imports should be used.
Version: 0.14.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 12
Error: testthat unit tests failed Execution halted ```
Version: 2.1.2
checking examples ... ERROR ``` Running examples in ‘inlabru-Ex.R’ failed The error most likely occurred in:
Name: cprod
Title: Cross product of integration points
Aliases: cprod
** Examples
Create integration points in dimension 'myDim' and 'myDiscreteDim'
ips1 = ipoints(c(0,8), name = "myDim") Error in loadNamespace(name) : there is no package called ‘INLA’ Calls: ipoints ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘INLA’
Version: 0.1.6
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > library(testthat) > library(internetarchive) > > test_check("internetarchive")
meta
not equal to reference from hecker_meta.rds
.
Different number of rowstestthat results ================================================================ OK: 21 SKIPPED: 0 FAILED: 1 1. Failure: ia_metadata() returns a data frame (@test-files-download.R#32)
Error: testthat unit tests failed Execution halted ```
Version: 2.0.0
checking re-building of vignette outputs ... WARNING ``` ... The following object is masked from 'package:base':
apply
Attaching package: 'GenomicAlignments'
The following object is masked from 'package:dplyr':
last
Attaching package: 'ShortRead'
The following object is masked from 'package:dplyr':
id
Error: processing vignette 'IONiseR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 3.6Mb
extdata 1.5Mb
checking R code for possible problems ... NOTE
...
‘start_time’
readFast5Summary.mc: no visible binding for global variable ‘duration’
readFast5Summary.mc: no visible binding for global variable
‘num_events’
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
‘baseCalledTemplate’
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
‘baseCalledComplement’
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
‘component’
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
‘idx’
show,Fast5Summary: no visible binding for global variable ‘full_2D’
show,Fast5Summary: no visible binding for global variable ‘pass’
Undefined global functions or variables:
:= AAAAA TTTTT accumulation baseCalledComplement baseCalledTemplate
bases_called category channel circleFun component duration error freq
full_2D group hour idx matrixCol matrixRow meanZValue mean_value
median_signal minute mux name nbases new_reads num_events oddEven
pass pentamer rbindlist readIDs seq_length start_time time_bin
time_group x y zvalue
Version: 1.4.0
...
isoSelect.IsomirDataSeq: no visible binding for global variable ‘freq’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘mir’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘mism’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘add’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘t5’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘t3’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘id’
isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global
variable ‘freq’
isoSelect,IsomirDataSeq: no visible binding for global variable ‘freq’
Undefined global functions or variables:
Count DB X1 X2 add af ambiguity average change condition current
enrich enrichGO error freq gene go group id mir mir_f mir_n mism
mism_f mism_n ngene pct_abundance reference rowMax rowMin sel_genes
t3 t5 term term_short type value y
Version: 0.1.5
Note: found 1 marked UTF-8 string
Version: 0.4.0
Namespace in Imports field not imported from: ‘readr’
All declared Imports should be used.
Version: 0.2.0
Note: found 188 marked UTF-8 strings
Version: 0.6.1
Package suggested but not available for checking: ‘magick’
Version: 0.1.1
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
20: map_lgl(df[keep_cols], is.list)
21: map_mold(.x, .f, logical(1), ...)
22: vapply(.x, .f, .mold, ..., USE.NAMES = FALSE)
23: df[keep_cols]
24:
[.keyed_df(df, keep_cols)
25:
keys<-(
tmp`, value = structure(list(vs = NA_real_, am = NA_real_), .Names = c("vs",
"am"), row.names = c(NA, -1L), class = c("tbl_df", "tbl", "data.frame")))
26: stop("Keys object should have the same number of rows as data.")
testthat results ================================================================ OK: 308 SKIPPED: 0 FAILED: 1 1. Error: distinct works (@test-keyed-df-one-tbl.R#298)
Error: testthat unit tests failed Execution halted ```
Version: 0.4.1
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘stringi’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 52458 marked UTF-8 strings
Version: 0.2.0
Namespaces in Imports field not imported from:
‘dplyr’ ‘tibble’
All declared Imports should be used.
Version: 1.0.0
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘memisc’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘memisc’
Version: 6.0-0
installed size is 7.5Mb
sub-directories of 1Mb or more:
data 7.2Mb
Version: 0.2
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘geojsonio’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘htmlwidgets’ ‘shiny’
All declared Imports should be used.
Version: 0.2
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘geojsonio’
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘shiny’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘boot’
All declared Imports should be used.
Version: 1.0.0
AnalyticalOptim: no visible global function definition for ‘optim’
LLConstructor : LL: no visible global function definition for ‘dpois’
MixtureDensity: no visible global function definition for ‘glm’
MixtureDensity : f_hat: no visible global function definition for
‘predict’
NullDensity : f0: no visible global function definition for ‘dpois’
Undefined global functions or variables:
dpois glm optim predict
Consider adding
importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
Version: 1.1.0
Installation failed.
See ‘/home/muelleki/git/R/dplyr/revdep/checks/loon/new/loon.Rcheck/00install.out’ for details.
* installing *source* package ‘loon’ ...
** package ‘loon’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Warning: no DISPLAY variable so Tk is not available
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: no DISPLAY variable so Tk is not available
Error: package or namespace load failed for ‘loon’:
.onLoad failed in loadNamespace() for 'loon', details:
call: structure(.External(.C_dotTcl, ...), class = "tclObj")
error: [tcl] couldn't connect to display "".
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/muelleki/git/R/dplyr/revdep/checks/loon/new/loon.Rcheck/loon’
* installing *source* package ‘loon’ ...
** package ‘loon’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Warning: no DISPLAY variable so Tk is not available
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: no DISPLAY variable so Tk is not available
Error: package or namespace load failed for ‘loon’:
.onLoad failed in loadNamespace() for 'loon', details:
call: structure(.External(.C_dotTcl, ...), class = "tclObj")
error: [tcl] couldn't connect to display "".
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/muelleki/git/R/dplyr/revdep/checks/loon/old/loon.Rcheck/loon’
Version: 1.0.1
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
setNames
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
Version: 1.4.1
installed size is 8.3Mb
sub-directories of 1Mb or more:
doc 2.6Mb
extdata 5.5Mb
Version: 0.3.1
Namespace in Imports field not imported from: ‘DBI’
All declared Imports should be used.
Version: 0.3.2
Package which this enhances but not available for checking: ‘geojsonio’
Version: 0.2.5
Packages unavailable to check Rd xrefs: ‘ggplot2’, ‘pander’, ‘pixiedust’
Version: 1.0.1
installed size is 9.0Mb
sub-directories of 1Mb or more:
data 3.2Mb
doc 4.9Mb
Version: 0.1.4
checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 5.4Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘tidyverse’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 2698 marked UTF-8 strings
Version: 1.8.1
checking installed package size ... NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
extdata 6.7Mb
checking R code for possible problems ... NOTE
.mgDb_annotateFeatures: no visible binding for global variable
‘db_keys’
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘index’
vignette_pheno_data: no visible global function definition for
‘read.csv’
Undefined global functions or variables:
. Keys db_keys index read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
Version: 0.3.3
Namespaces in Imports field not imported from:
‘data.table’ ‘foreach’
All declared Imports should be used.
Version: 0.2.7
checking tests ... ``` ERROR Running the tests in ‘tests/testthat-a.R’ failed. Last 13 lines of output:
Failure: mnis_additional returns expected format (@test_additional.R#80) ----
xi
has length 296, not length 285.
Failure: mnis_extra returns expected format (@test_extra.R#10) --------------
xmnise
has length 192, not length 188.
testthat results ================================================================ OK: 97 SKIPPED: 0 FAILED: 2 1. Failure: mnis_additional returns expected format (@test_additional.R#80) 2. Failure: mnis_extra returns expected format (@test_extra.R#10)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.1
Packages unavailable to check Rd xrefs: ‘lme4’, ‘rstanarm’
Version: 0.1.3
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning: Deprecated
Quitting from lines 112-115 (modeval.Rmd)
Error: processing vignette 'modeval.Rmd' failed with diagnostics:
the argument has already been evaluated
Execution halted
Version: 1.2.2
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 2.3Mb
Version: 1.0.1
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘MonetDBLite’
checking dependencies in R code ... NOTE
Missing or unexported objects:
‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
‘dplyr::tbl_sql’
Version: 0.5.0
checking installed package size ... NOTE
installed size is 18.9Mb
sub-directories of 1Mb or more:
libs 18.6Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Version: 0.1.3
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: out$push(condition) invokeRestart("muffleMessage") }) 4: monkeylearn_extract(request = c(" ", "I do not know what the horse is doing in the house")) 5: monkeylearn_check(output) 6: stop("HTTP failure: ", req$status_code, "\n", content(req)$detail, call. = FALSE)
testthat results ================================================================ OK: 4 SKIPPED: 0 FAILED: 3 1. Error: monkeylearn_parse returns a data.frame with a data.frame as attribute (@test_output.R#7) 2. Error: No error if no results from the extractor call (@test_output.R#55) 3. Error: Blank texts are handled properly (@test_text_size.R#10)
Error: testthat unit tests failed Execution halted ```
Version: 2.4.0
checking re-building of vignette outputs ... WARNING
...
the condition has length > 1 and only the first element will be used
Warning in if (method == "num_genes") { :
the condition has length > 1 and only the first element will be used
Warning in if (method == "num_genes") { :
the condition has length > 1 and only the first element will be used
Warning in if (method == "num_genes") { :
the condition has length > 1 and only the first element will be used
Warning in if (method == "num_genes") { :
the condition has length > 1 and only the first element will be used
Warning in if (method == "num_genes") { :
the condition has length > 1 and only the first element will be used
Warning: Deprecated, use tibble::rownames_to_column() instead.
Warning: Removed 3576038 rows containing non-finite values (stat_density).
Warning: Deprecated, use tibble::rownames_to_column() instead.
Warning: Deprecated, use tibble::rownames_to_column() instead.
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous y-axis
Quitting from lines 327-334 (monocle-vignette.Rnw)
Error: processing vignette 'monocle-vignette.Rnw' failed with diagnostics:
BLAS/LAPACK routine 'DLASCL' gave error code -4
Execution halted
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’
clusterCells: no visible binding for global variable ‘rho’
clusterCells: no visible binding for global variable ‘delta’
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’
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
‘next_node’
get_next_node_id: no visible binding for global variable ‘next_node’
make_canonical: no visible global function definition for ‘nei’
measure_diameter_path: no visible global function definition for ‘nei’
orderCells: no visible binding for '<<-' assignment to ‘next_node’
project2MST: no visible global function definition for ‘nei’
Undefined global functions or variables:
Size_Factor delta nei next_node rho
Version: 1.1.0
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘manipulate’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘cubature’
Version: 0.14.0
Note: found 7 marked UTF-8 strings
Version: 0.3.0
Namespaces in Imports field not imported from:
‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
All declared Imports should be used.
Version: 3.1.0
installed size is 6.9Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 4.5Mb
Version: 0.8.10
idata <- dplyr::mutate(idata, GRP = ID %%2)
idata
ID end delta add GRP
1 1 24 6 1 2 2 48 6 0 3 3 72 6 1 4 4 96 6 0
l <- as_deslist(idata,"GRP") Error: distinct() does not support columns of type
list
Execution halted ```
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.7Mb
Version: 0.1.2
Version: 1.10.0
...
.read_mzIDs.mzR.engine.single.file: no visible binding for global
variable ‘modification’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
variable ‘DatabaseAccess’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
variable ‘DatabaseDescription’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
variable ‘DBseqLength’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
global variable ‘accession’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
global variable ‘pepSeq’
recalibrate,MSnID: no visible global function definition for ‘median’
recalibrate,MSnID: no visible global function definition for ‘density’
Undefined global functions or variables:
DBseqLength DatabaseAccess DatabaseDescription accession density i
location mass median modification name optim pepSeq quantile rnorm
spectrumID
Consider adding
importFrom("stats", "density", "median", "optim", "quantile", "rnorm")
to your NAMESPACE file.
Version: 1.0.0
Namespaces in Imports field not imported from:
‘hms’ ‘methods’
All declared Imports should be used.
Version: 0.6.0
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 2.0Mb
doc 2.7Mb
Version: 0.2.1
checking package dependencies ... ERROR ``` Packages required but not available: ‘autothresholdr’ ‘EBImage’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 0.1.0
Note: found 5 marked UTF-8 strings
Version: 1.2.0
checking re-building of vignette outputs ... WARNING ``` ...
Warning: executing %dopar% sequentially: no parallel backend registered Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'
Error: processing vignette 'netprioR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
Version: 0.5.0
checking examples ... ERROR ``` ... > require(psych) Loading required package: psych
Attaching package: ‘psych’
The following object is masked from ‘package:neuropsychology’:
describe
The following objects are masked from ‘package:ggplot2’:
%+%, alpha
df <- select_numeric(personality) fa <- psych::fa(df)
fa_loadings(fa)$max Error in typeof(x) : argument "vars" is missing, with no default Calls: fa_loadings ... vars_select_eval -> scoped_vars -> poke_vars -> is_null -> typeof Execution halted ```
Namespaces in Imports field not imported from:
‘htmlTable’ ‘lme4’ ‘stringi’
All declared Imports should be used.
Version: 0.99.2
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘NFPdata’
checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
data 7.5Mb
Version: 0.9.0-1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 195 SKIPPED: 0 FAILED: 11
Error: testthat unit tests failed Execution halted ```
checking compiled code ... WARNING ``` File ‘nlmixr/libs/nlmixr.so’: Found ‘__assert_fail’, possibly from ‘assert’ (C) Objects: ‘RcppExportMod.o’, ‘RcppExports.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking installed package size ... NOTE
installed size is 13.7Mb
sub-directories of 1Mb or more:
libs 12.5Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘dparser’ ‘inline’ ‘n1qn1’
All declared Imports should be used.
Version: 0.1.0
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘hurricaneexposuredata’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
‘forcats’ ‘hurricaneexposure’ ‘plyr’
All declared Imports should be used.
Version: 1.1.0
Package unavailable to check Rd xrefs: ‘bipartite’
Version: 0.3.1
...
reg_dist: no visible global function definition for ‘lm’
resid_boot: no visible global function definition for ‘resid’
resid_pboot: no visible global function definition for ‘rnorm’
resid_rotate: no visible global function definition for ‘rnorm’
resid_rotate: no visible global function definition for ‘update’
resid_rotate: no visible global function definition for ‘resid’
resid_sigma: no visible global function definition for ‘rnorm’
rorschach: no visible global function definition for ‘rbinom’
rss: no visible global function definition for ‘resid’
sep_dist: no visible global function definition for ‘dist’
sep_dist: no visible global function definition for ‘cutree’
sep_dist: no visible global function definition for ‘hclust’
uni_dist: no visible global function definition for ‘sd’
Undefined global functions or variables:
coef cutree dist filter hclust lm predict quantile rbinom resid rnorm
sd update
Consider adding
importFrom("stats", "coef", "cutree", "dist", "filter", "hclust", "lm",
"predict", "quantile", "rbinom", "resid", "rnorm", "sd",
"update")
to your NAMESPACE file.
Version: 0.2.2
installed size is 7.0Mb
sub-directories of 1Mb or more:
data 6.9Mb
Version: 0.4.0
Note: found 6409 marked UTF-8 strings
Version: 0.1.2
Packages unavailable to check Rd xrefs: ‘ensurer’, ‘validate’
Version: 2.5
Note: found 4 marked UTF-8 strings
Version: 0.1.8
checking examples ... ERROR ``` Running examples in ‘officer-Ex.R’ failed The error most likely occurred in:
Name: slip_in_img
Title: append an image
Aliases: slip_in_img
** Examples
library(magrittr) img.file <- file.path( Sys.getenv("R_HOME"), "doc", "html", "logo.jpg" ) x <- read_docx() %>% + body_add_par("R logo: ", style = "Normal") %>% + slip_in_img(src = img.file, style = "strong", width = .3, height = .3) Error: file.exists(src) is not TRUE Execution halted ```
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
6: freduce(value,
_function_list`)
7: withVisible(function_list[k])
8: function_list[k]
9: ph_with_img(., type = "body", src = img.file, height = 1.06, width = 1.39)
10: external_img(src, width = width/914400, height = height/914400)
11: stopifnot(file.exists(src))
12: stop(msg, call. = FALSE, domain = NA)
testthat results ================================================================ OK: 341 SKIPPED: 1 FAILED: 2 1. Error: image add (@test-docx-add.R#68) 2. Error: add img into placeholder (@test-pptx-add.R#67)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 180-190 (powerpoint.Rmd) Error: processing vignette 'powerpoint.Rmd' failed with diagnostics: file.exists(src) is not TRUE Execution halted ```
Version: 2.6.0
installed size is 11.0Mb
sub-directories of 1Mb or more:
doc 5.4Mb
libs 4.9Mb
Version: 0.2.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: > library("testthat") > test_check("openadds") Loading required package: openadds
testthat results ================================================================ OK: 47 SKIPPED: 0 FAILED: 1 1. Failure: oa_search works (@test-oa_search.R#39)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.2
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
3:
_f`(placename = placename, key = key, bounds = bounds, countrycode = countrycode,
language = language, limit = limit, min_confidence = min_confidence, no_annotations = no_annotations,
no_dedupe = no_dedupe, no_record = no_record, abbrv = abbrv)
4: opencage_check(temp)
5: stop("HTTP failure: ", req$status_code, "\n", message, call. = FALSE)
testthat results ================================================================ OK: 23 SKIPPED: 0 FAILED: 4 1. Error: opencage_parse returns what it should for both functions (@test-opencage_parse.R#6) 2. Error: opencage_parse returns what it should for both functions with several parameters (@test-opencage_parse.R#40) 3. Error: opencage_parse deals well with resuls being NULL (@test-opencage_parse.R#72) 4. Error: the bounds argument is well taken into account (@test-opencage_parse.R#86)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 41-47 (opencage.Rmd)
Error: processing vignette 'opencage.Rmd' failed with diagnostics:
HTTP failure: 403
Invalid or missing api key (forbidden)
Execution halted
Version: 0.1.4
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 0.1.0
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 22-24 (openwindfarm-vignette.Rmd)
Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Version: 1.2.2
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Error: processing vignette 'Organism.dplyr.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::smartKeys’ ‘GenomicFeatures:::.exons_with_3utr’
‘GenomicFeatures:::.exons_with_5utr’
‘GenomicFeatures:::get_TxDb_seqinfo0’
‘S4Vectors:::extract_data_frame_rows’
See the note in ?`:::` about the use of this operator.
Version: 0.2.1
Note: found 13 marked UTF-8 strings
Version: 0.1.0
checking examples ... ERROR ``` Running examples in ‘parsemsf-Ex.R’ failed The error most likely occurred in:
Name: make_area_table
Title: Make a table of peptide areas
Aliases: make_area_table
** Examples
make_area_table(parsemsf_example("test_db.msf")) Error: Condition message must be a string Execution halted ```
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
13: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with
install.packages(\"{name}\")`")
14: .abort(text)
15: cnd_error(type, .msg = msg, .call = sys.call(-1))
16: new_cnd(c(.type, "error"), ..., .msg = .msg)
17: stop("Condition message must be a string", call. = FALSE)
Error: Condition message must be a string testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 3 1. Error: make_area_table creates a data frame with the correct column names (@test_make_area_table.R#16) 2. Error: make_pep_table creates a data frame with the correct column names (@test_make_pep_table.R#13) 3. Error: map_peptides creates a data frame with the correct column names (@test_map_peptides.R#16)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 20-25 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Condition message must be a string
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RSQLite’
All declared Imports should be used.
Version: 1.2.1
Error in re-building vignettes:
...
Warning: Transformation introduced infinite values in discrete y-axis
Error: processing vignette 'PathoStatAdvanced.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
Version: 0.2
GNU make is a SystemRequirements.
Version: 1.0.0
Namespaces in Imports field not imported from:
‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’
All declared Imports should be used.
Version: 0.1.1
Namespaces in Imports field not imported from:
‘Rgraphviz’ ‘cluster’ ‘graph’
All declared Imports should be used.
Version: 1.2.0
checking re-building of vignette outputs ... WARNING ``` ...
intersect, setdiff, setequal, union
Found more than one class "phylo" in cache; using the first, from namespace 'treeio' Also defined by 'phyloseq' Found more than one class "phylo" in cache; using the first, from namespace 'treeio' Also defined by 'phyloseq'
Attaching package: 'tidyr'
The following object is masked from 'package:ggtree':
expand
The following object is masked from 'package:Matrix':
expand
Error: processing vignette 'philr-intro.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE
name.balance: no visible global function definition for ‘as’
vote.annotation: no visible global function definition for ‘is’
Undefined global functions or variables:
as is
Consider adding
importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘compositions’
Version: 1.8.2
Package suggested but not available for checking: ‘ggsubplot’
Version: 0.8.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Provenance hash a generated on b with c. testthat results ================================================================ OK: 1024 SKIPPED: 0 FAILED: 1 1. Failure: provenance (@test-provenance.R#7)
Error: testthat unit tests failed Execution halted ```
Version: 2.0.0
Namespace in Imports field not imported from: ‘purrr’
All declared Imports should be used.
Version: 1.5
checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
data 6.0Mb
checking data for non-ASCII characters ... NOTE
Note: found 7256 marked UTF-8 strings
Version: 0.1
Namespaces in Imports field not imported from:
‘Hmisc’ ‘digest’ ‘htmltools’ ‘knitr’ ‘lazyWeave’ ‘lubridate’ ‘rJava’
All declared Imports should be used.
Version: 0.0-3
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘ISOcodes’
checking data for non-ASCII characters ... NOTE
Note: found 8 marked UTF-8 strings
Version: 0.1.0
Namespace in Imports field not imported from: ‘testthat’
All declared Imports should be used.
Version: 0.1.0
Note: found 2 marked UTF-8 strings
Version: 1.16.1
checking re-building of vignette outputs ... WARNING ``` ...
nChrom
Loading required package: cluster Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
This is pRoloc version 1.16.1 Read '?pRoloc' and references therein for information about the package and how to get started.
This is pRolocdata version 1.14.0. Use 'pRolocdata()' to list available data sets. Loading required namespace: GO.db
Loading required package: GO.db Retaining 84 out of 524 in GOAnnotations Retaining 79 out of 84 in GOAnnotations Error: processing vignette 'pRoloc-goannotations.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
doc 3.3Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’
‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’
‘caret:::predict.plsda’
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:
‘checkSortedFeatureNames’ ‘opt’
checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘pRoloc/R/annotation.R’:
unlockBinding("params", .pRolocEnv)
checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
Version: 1.10.0
checking whether package ‘pRolocGUI’ can be installed ... WARNING
Found the following significant warnings:
Warning: namespace ‘lme4’ is not available and has been replaced
Warning: namespace ‘MatrixModels’ is not available and has been replaced
See ‘/home/muelleki/git/R/dplyr/revdep/checks/pRolocGUI/new/pRolocGUI.Rcheck/00install.out’ for details.
checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Lisa Breckels <lms79@cam.ac.uk> [aut, cre]
Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘pRoloc:::remap’
See the note in ?`:::` about the use of this operator.
Version: 0.2.1
installed size is 22.9Mb
sub-directories of 1Mb or more:
libs 21.7Mb
Version: 1.12.3
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Error: processing vignette 'proteoQC.Rmd' failed with diagnostics:
there is no package called ‘prettydoc’
Execution halted
checking installed package size ... NOTE
installed size is 8.0Mb
sub-directories of 1Mb or more:
doc 3.2Mb
extdata 4.0Mb
checking R code for possible problems ... NOTE
...
plotMS2boxplot: no visible binding for global variable ‘techRep’
plotMS2boxplot: no visible binding for global variable ‘fraction’
plotMS2boxplot: no visible binding for global variable ‘MS2QC’
plotSampleIDResultErrorBar: no visible binding for global variable
‘fraction’
plotSampleIDResultErrorBar: no visible binding for global variable
‘val’
plotSampleIDResultErrorBar: no visible binding for global variable ‘se’
plotSampleVenn: no visible global function definition for ‘grid.draw’
plotTechRepVenn : <anonymous>: no visible global function definition
for ‘grid.draw’
qcHist: no visible binding for global variable ‘error’
qcHist: no visible binding for global variable ‘techRep’
qcHist: no visible binding for global variable ‘bioRep’
qcHist2: no visible binding for global variable ‘error’
qcHist2: no visible binding for global variable ‘fractile’
Undefined global functions or variables:
..count.. Intensity MS1QC MS2QC TMT10 TMT6 Tag V1 V2 V3 V4 V5 bioRep
curenv delta error exprs fractile fraction grid.draw iTRAQ4 iTRAQ8
label peplength peptide_summary precursorCharge quantify ratio
readMgfData se techRep val x y
Version: 0.2.1
Note: found 20105 marked UTF-8 strings
Version: 0.1.1
Note: found 5 marked UTF-8 strings
Version: 0.0.2
Namespaces in Imports field not imported from:
‘rtf’ ‘tidyverse’
All declared Imports should be used.
Version: 0.0.3
installed size is 5.3Mb
sub-directories of 1Mb or more:
dict 5.1Mb
Version: 0.0.2
Namespace in Imports field not imported from: ‘lazyeval’
All declared Imports should be used.
Version: 2.2.8
Package unavailable to check Rd xrefs: ‘gplots’
Version: 0.1.0
Package unavailable to check Rd xrefs: ‘rgl’
Version: 0.1.0
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 92-106 (wilcox1973.Rmd)
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Version: 1.4.0
installed size is 12.1Mb
sub-directories of 1Mb or more:
extdata 9.7Mb
libs 1.9Mb
Version: 0.6.2
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘Hmisc’
checking data for non-ASCII characters ... NOTE
Note: found 4145 marked UTF-8 strings
Version: 1.5.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘psych’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘PredictABEL’
Version: 0.1.0
Namespaces in Imports field not imported from:
‘MCMCpack’ ‘gridExtra’ ‘knitr’
All declared Imports should be used.
Version: 0.2.4
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'summary_table': ‘cbind.qwraps2_summary_table’
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. ```
Version: 0.1.2
Namespaces in Imports field not imported from:
‘data.table’ ‘dplyr’ ‘lmerTest’
All declared Imports should be used.
Version: 0.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 139 SKIPPED: 0 FAILED: 10
Error: testthat unit tests failed Execution halted ```
Version: 0.8.0
Note: found 2 marked UTF-8 strings
Version: 0.8.0
Note: found 1 marked UTF-8 string
Version: 0.9
Namespaces in Imports field not imported from:
‘MASS’ ‘dtplyr’
All declared Imports should be used.
Version: 0.0.5
checking package dependencies ... NOTE
Packages suggested but not available for checking: ‘gurobi’ ‘rgurobi’
checking installed package size ... NOTE
installed size is 17.9Mb
sub-directories of 1Mb or more:
data 3.6Mb
libs 13.1Mb
Version: 1.12.0
checking examples ... WARNING ``` Found the following significant warnings:
Warning: 'rbind_all' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 5.2Mb
checking R code for possible problems ... NOTE
tallyBamRegion: no visible global function definition for 'PileupParam'
tallyBamRegion: no visible global function definition for
'ScanBamParam'
tallyBamRegion: no visible global function definition for 'pileup'
Undefined global functions or variables:
PileupParam ScanBamParam pileup
checking installed files from ‘inst/doc’ ... NOTE ``` The following files should probably not be installed: ‘rariant-inspect-ci.png’, ‘rariant-inspect-shift.png’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. ```
Version: 5.1.0
checking re-building of vignette outputs ... WARNING
``
Error in re-building vignettes:
...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'rattle.tex' failed.
LaTeX errors:
! LaTeX Error: File
algorithm2e.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty)
! Emergency stop.
l.14 \usepackage [^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘gWidgetsRGtk2’ ‘playwith’
checking dependencies in R code ... NOTE ```
(R:71248): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() ```
Version: 1.2-3
checking installed package size ... NOTE
installed size is 27.7Mb
sub-directories of 1Mb or more:
libs 26.4Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘lme4’
All declared Imports should be used.
Version: 0.5.4
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 37 SKIPPED: 0 FAILED: 3 1. Failure: bison returns the correct value (@test-bison.R#16) 2. Failure: bison_tax returns the correct ... (@test-bison_tax.R#12) 3. Failure: bison_tax returns the correct ... (@test-bison_tax.R#14)
Error: testthat unit tests failed Execution halted ```
Version: 0.3.7
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 0.2.1
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rcongresso)
>
> test_check("rcongresso")
Error: Column `id` must be a 1d atomic vector or a list
In addition: Warning message:
Unknown or uninitialised column: 'id'.
testthat results ================================================================
OK: 18 SKIPPED: 0 FAILED: 0
Execution halted
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 45-50 (introducao-rcongresso.Rmd)
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Column id
must be a 1d atomic vector or a list
Execution halted
```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
Version: 0.7.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:
warnings
does not match "500: java.lang.NumberFormatException: For input string: \"323234343434\"".
Actual values:testthat results ================================================================ OK: 218 SKIPPED: 0 FAILED: 3 1. Failure: DOIs with no agency found still work, at least some do (@test_cr_cn.R#38) 2. Failure: cr_members fails correctly (@test_cr_members.R#43) 3. Failure: cr_members fails correctly (@test_cr_members.R#47)
Error: testthat unit tests failed Execution halted ```
Version: 0.2.1
Note: found 6543 marked UTF-8 strings
Version: 0.8.1
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
2: In checkSkipLoopCntxt(a, cntxt, breakOK) :
closing unused connection 4 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_b300d02b-fd51-4ee6-9c5e-ea58e097960c_rdrop2_package_test_drop.png)
3: In checkSkipLoopCntxt(a, cntxt, breakOK) :
closing unused connection 3 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_b1e9bd54-d694-4b30-91b7-9703e85ebb10_file-ops.csv)
4: In inherits(x, "factor") :
closing unused connection 8 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_aa7c5330-af59-47a4-8a2b-fdb175cd3541_share.csv)
5: In inherits(x, "factor") :
closing unused connection 7 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_5abe876b-01a1-4f24-b878-34d06daf8c96_delete.csv)
6: In inherits(x, "factor") :
closing unused connection 6 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_678ca208-5c06-4dcc-b7a6-391db9674494_move.csv)
7: In inherits(x, "factor") :
closing unused connection 5 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_793b2ceb-6ccd-4963-88d1-b48c4fcdbb7c_iris-test-copy.csv)
8: In inherits(x, "factor") :
closing unused connection 4 (/home/muelleki/git/R/dplyr/revdep/checks/rdrop2/new/rdrop2.Rcheck/tests/testthat/rdrop2_package_test_b52cccf1-be04-49ec-8cc6-983cb9f82c5e_test-drop_download.csv)
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘digest’
All declared Imports should be used.
Version: 1.2.1
sfread: no visible binding for global variable ‘header’
sfread: no visible binding for global variable ‘nrows’
Undefined global functions or variables:
header nrows
Version: 0.3.0
installed size is 7.4Mb
sub-directories of 1Mb or more:
doc 2.5Mb
libs 4.8Mb
Version: 0.9.8
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 551 SKIPPED: 0 FAILED: 33
Error: testthat unit tests failed Execution halted ```
Version: 0.9.0
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘magick’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RSQLite’ ‘dbplyr’
All declared Imports should be used.
Version: 0.12.0
Packages which this enhances but not available for checking:
‘data.table’ ‘htmlwidgets’
Version: 0.4.2
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 91 SKIPPED: 0 FAILED: 15
Error: testthat unit tests failed Execution halted ```
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘taxize’
Version: 2.1.2
Note: found 44 marked UTF-8 strings
Version: 0.3.3
checking package dependencies ... ERROR ``` Package required but not available: ‘geojsonio’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.2.6
installed size is 5.2Mb
sub-directories of 1Mb or more:
java 4.5Mb
Version: 0.3.0
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
Version: 2.0.7
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
Version: 1.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Content type 'text/html; charset=utf-8' length 504270 bytes (492 KB) ================================================== downloaded 492 KB
testthat results ================================================================ OK: 112 SKIPPED: 0 FAILED: 6 1. Failure: nhanes_search on variables passes spot check (@test_search.R#13) 2. Failure: nhanes_search on variables passes spot check (@test_search.R#14) 3. Failure: nhanes_search on files passes spot check (@test_search.R#20) 4. Failure: nhanes_search on files passes spot check (@test_search.R#21) 5. Failure: fuzzy search works on files (@test_search.R#33) 6. Failure: fuzzy search works on files (@test_search.R#34)
Error: testthat unit tests failed Execution halted ```
Version: 0.7.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 176 SKIPPED: 1 FAILED: 11
Error: testthat unit tests failed Execution halted ```
Version: 0.99.6
Namespace in Imports field not imported from: ‘data.table’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘matrixcalc’
All declared Imports should be used.
Version: 0.2.2
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 34-48 (using_openair_package_with_openaq_data.Rmd) Error: processing vignette 'using_openair_package_with_openaq_data.Rmd' failed with diagnostics: uh oh, the OpenAQ API seems to be having some issues, try again later Execution halted ```
Version: 0.2.2
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 15: check_values(data, values = values, unique = TRUE, nulls = FALSE, data_name = data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-data3.R:33 16: check_data_values(data, values, data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-values.R:20 17: vapply(column_names, FUN = check_data_values_column, logical(1), data = data, values = values, data_name = data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-data-values.R:20 18: FUN(X[[i]], ...) 19: check_vector_value_missing(vector, value, column_name, data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-data-values.R:9 20: error(name_info(column_name, data_name), " cannot include missing values") at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-vector-value.R:7 21: stop(..., call. = FALSE) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/utils.R:20
testthat results ================================================================ OK: 1 SKIPPED: 0 FAILED: 1 1. Error: download_pdo (@test-download-pdo.R#4)
Error: testthat unit tests failed Execution halted ```
Version: 0.2.0
Package which this enhances but not available for checking: ‘shiny’
Version: 1.2
GNU make is a SystemRequirements.
Version: 1.0.0
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 0.5.0
Error in re-building vignettes:
...
Quitting from lines 22-29 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Missing API key; ?sc_key for details
Execution halted
Version: 0.3.0
checking examples ... ERROR ``` Running examples in ‘rsoi-Ex.R’ failed The error most likely occurred in:
Name: download_enso
Title: Download Southern Oscillation Index and Oceanic Nino Index data
Aliases: download_enso
** Examples
enso <- download_enso() Error in open.connection(con, "rb") : Timeout was reached: Resolving timed out after 10000 milliseconds Calls: download_enso ... structure -> read_connection -> open -> open.connection Execution halted ```
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
Version: 0.2.2
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 7: compareVersion(currentRow$spark, "2.0")
testthat results ================================================================ OK: 1 SKIPPED: 0 FAILED: 8 1. Error: Test transformation from h2o frame to data frame (@test_transforms.R#5) 2. Error: Test transformation of a spark data_frame of bools to an h2o frame of bools (@test_transforms.R#17) 3. Error: Test transformation of a spark data_frame of complex types to an h2o frame of complex types (@test_transforms.R#29) 4. Error: Test transformation of a spark data_frame of float types to an h2o frame of floats (@test_transforms.R#43) 5. Error: Test transformation of a spark data_frame of int types to an h2o frame of ints (@test_transforms.R#54) 6. Error: Test transformation of a spark data_frame of str types to an h2o frame of str (@test_transforms.R#65) 7. Error: Test transformation from dataframe to h2o frame (@test_transforms.R#76) 8. Error: Test transformation from dataframe to h2o frame (@test_transforms.R#86)
Error: testthat unit tests failed Execution halted ```
Version: 0.6.1
installed size is 5.0Mb
sub-directories of 1Mb or more:
libs 2.7Mb
Version: 0.1.0
Note: found 18627 marked UTF-8 strings
Version: 1.6.0
checking examples ... ERROR ``` ...
MET|4233
) %>% boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "cohort", "MET") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "cohort", "log1p(MET)") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), max)", "log1p(MET)") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
facet example
library(RTCGA.mutations) Error in library(RTCGA.mutations) : there is no package called ‘RTCGA.mutations’ Execution halted ```
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘RTCGA.clinical’ ‘RTCGA.mutations’ ‘RTCGA.RPPA’ ‘RTCGA.mRNA’
‘RTCGA.miRNASeq’ ‘RTCGA.methylation’ ‘RTCGA.CNV’
checking R code for possible problems ... NOTE
availableDates: no visible binding for global variable ‘.’
downloadTCGA: no visible binding for global variable ‘.’
ggbiplot: no visible binding for global variable ‘xvar’
ggbiplot: no visible binding for global variable ‘yvar’
ggbiplot: no visible global function definition for ‘muted’
ggbiplot: no visible binding for global variable ‘varname’
ggbiplot: no visible binding for global variable ‘angle’
ggbiplot: no visible binding for global variable ‘hjust’
read.mutations: no visible binding for global variable ‘.’
read.rnaseq: no visible binding for global variable ‘.’
survivalTCGA: no visible binding for global variable ‘times’
whichDateToUse: no visible binding for global variable ‘.’
Undefined global functions or variables:
. angle hjust muted times varname xvar yvar
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘RTCGA.clinical’, ‘RTCGA.mutations’, ‘RTCGA.CNV’, ‘RTCGA.RPPA’, ‘RTCGA.mRNA’, ‘RTCGA.miRNASeq’, ‘RTCGA.methylation’
Version: 0.5.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 6: Filter(Negate(is.null), x) 7: unlist(lapply(x, f)) 8: lapply(x, f) 9: check_key(key) 10: stop("need an API key for ", y, call. = FALSE)
testthat results ================================================================ OK: 2 SKIPPED: 0 FAILED: 4 1. Error: returns the correct stuff (@test-as_search.R#8) 2. Error: returns the correct stuff (@test-geo_search.R#8) 3. Failure: fails well (@test-geo_search.R#48) 4. Error: fails well (@test-geo_search.R#50)
Error: testthat unit tests failed Execution halted ```
Version: 1.3
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 0.6.2
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: grepl("Bufo debilis", aa$data$scientificname) isn't true.
testthat results ================================================================ OK: 107 SKIPPED: 0 FAILED: 3 1. Failure: searchbyterm works correctly (@test-searchbyterm.R#12) 2. Failure: vert_id works (@test-vert_id.R#15) 3. Failure: vert_id works (@test-vert_id.R#33)
Error: testthat unit tests failed Execution halted ```
Version: 0.6-1
Package suggested but not available for checking: ‘SnakeCharmR’
Version: 0.1.0
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
Version: 1.0.0
checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 6.3Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘gamlss.dist’
All declared Imports should be used.
Version: 1.4.0
checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
doc 5.7Mb
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'arrange': ‘arrange.SCESet’
S3 methods shown with full name in documentation object 'filter': ‘filter.SCESet’
S3 methods shown with full name in documentation object 'mutate': ‘mutate.SCESet’
S3 methods shown with full name in documentation object 'rename': ‘rename.SCESet’
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. ```
Version: 1.0
Namespaces in Imports field not imported from:
‘Rcpp’ ‘testthat’
All declared Imports should be used.
Version: 1.3.4
Namespaces in Imports field not imported from:
‘cluster’ ‘factoextra’ ‘tidyr’
All declared Imports should be used.
Version: 0.1.5
Namespace in Imports field not imported from: ‘datasets’
All declared Imports should be used.
Version: 0.5.2
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 2: httr::POST(sprintf("%s/query.json", drill_server), encode = "json", body = list(queryType = "SQL", query = query)) 3: request_perform(req, hu$handle$handle) 4: request_fetch(req$output, req$url, handle) 5: request_fetch.write_memory(req$output, req$url, handle) 6: curl::curl_fetch_memory(url, handle = handle)
testthat results ================================================================ OK: 1 SKIPPED: 0 FAILED: 3 1. Error: Core dbplyr ops work (@test-sergeant.R#12) 2. Failure: REST API works (@test-sergeant.R#25) 3. Error: REST API works (@test-sergeant.R#27)
Error: testthat unit tests failed Execution halted ```
Version: 2.1.0
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.0Mb
Version: 0.5-5
checking examples ... ERROR ``` ... The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
nc = st_read(system.file("shape/nc.shp", package="sf")) Reading layer
nc' from data source
/home/muelleki/git/R/dplyr/revdep/checks/sf/new/sf.Rcheck/sf/shape/nc.shp' using driver `ESRI Shapefile' Simple feature collection with 100 features and 14 fields geometry type: MULTIPOLYGON dimension: XY bbox: xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965 epsg (SRID): 4267 proj4string: +proj=longlat +datum=NAD27 +no_defs nc %>% filter(AREA > .1) %>% plot() Warning: plotting the first 10 out of 14 attributes; use max.plot = 14 to plot allplot 10 smallest counties in grey:
st_geometry(nc) %>% plot() nc %>% select(AREA) %>% arrange(AREA) %>% slice(1:10) %>% plot(add = TRUE, col = 'grey') title("the ten counties with smallest area") nc[c(1:100, 1:10), ] %>% distinct() %>% nrow() Error: distinct() does not support columns of type
list
Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 194-197 (sf5.Rmd)
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
checking installed package size ... NOTE
installed size is 20.2Mb
sub-directories of 1Mb or more:
doc 10.7Mb
libs 5.7Mb
sqlite 1.5Mb
Version: 0.1.8
Note: found 2 marked UTF-8 strings
Version: 0.2.1
installed size is 9.9Mb
sub-directories of 1Mb or more:
www 9.7Mb
Version: 0.1.0
Namespaces in Imports field not imported from:
‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
All declared Imports should be used.
Version: 2.1.3
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘viridis’
All declared Imports should be used.
Version: 0.2.2
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 0.2.4
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 3.6.4
installed size is 12.3Mb
sub-directories of 1Mb or more:
doc 1.0Mb
libs 10.9Mb
Version: 1.0.5
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘sjPlot’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘sjPlot’
Version: 2.6.2
Package suggested but not available for checking: ‘sjPlot’
Version: 2.4.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘prediction’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘plm’
Version: 0.12.0
Packages unavailable to check Rd xrefs: ‘sjPlot’, ‘MuMIn’, ‘piecewiseSEM’
Version: 1.0.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 193 SKIPPED: 0 FAILED: 26
Error: testthat unit tests failed Execution halted ```
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘XML’
Version: 0.7.0
Note: found 1320 marked UTF-8 strings
Version: 0.7.26
...
regression_plot: no visible global function definition for
‘colorRampPalette’
regression_plot: no visible global function definition for
‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
for ‘pnorm’
regression_plot: no visible global function definition for
‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
colorRampPalette density flush.console loess loess.control pnorm
predict quantile read.csv
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "density", "loess", "loess.control", "pnorm",
"predict", "quantile")
importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Version: 1.0.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 18 SKIPPED: 0 FAILED: 8 1. Failure: HaldDP model construction (@testHaldDP.R#106) 2. Failure: HaldDP model construction (@testHaldDP.R#108) 3. Failure: HaldDP model construction (@testHaldDP.R#109) 4. Failure: HaldDP model construction (@testHaldDP.R#110) 5. Failure: HaldDP model construction (@testHaldDP.R#116) 6. Failure: Test time/location data structures (@testHaldDPTimeLoc.R#107) 7. Failure: Prior and init (@testHaldDPTimeLoc.R#194) 8. Failure: Prior and init (@testHaldDPTimeLoc.R#195)
Error: testthat unit tests failed Execution halted ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘gtools’ ‘hashmap’ ‘reshape2’
All declared Imports should be used.
Version: 0.1.0
checking whether package ‘SpaDES.core’ can be installed ... WARNING
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/dplyr/revdep/checks/SpaDES.core/new/SpaDES.core.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘CircStats’ ‘RandomFields’ ‘grDevices’ ‘sp’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘fastdigest’
All declared Imports should be used.
Version: 0.6.4
Version: 0.3.3.1
checking re-building of vignette outputs ... WARNING
``
Error in re-building vignettes:
...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'sparseHessianFD.tex' failed.
LaTeX errors:
! LaTeX Error: File
algorithm.sty' not found.
Type X to quit or to proceed, or enter new name. (Default extension: sty)
! Emergency stop.
l.27 \usepackage {algorithmic}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```
Version: 0.3
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
All declared Imports should be used.
Version: 0.9.5
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/dplyr/revdep/checks/ss3sim/new/ss3sim.Rcheck/00install.out’ for details.
Version: 0.5.3
checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 0.1.0
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘dplyr’ ‘magrittr’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 34 marked UTF-8 strings
Version: 0.4.1
installed size is 8.1Mb
Version: 0.1.5
Package unavailable to check Rd xrefs: ‘distrEx’
Version: 0.3.0
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(statisticalModeling)
Loading required package: ggplot2
>
> test_check("statisticalModeling")
Error: gwm() has been removed from `mosaic'.
It will be replaced by better tools in `mosaicModel'.
testthat results ================================================================
OK: 21 SKIPPED: 0 FAILED: 0
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 303-306 (modeling.Rmd)
Error: processing vignette 'modeling.Rmd' failed with diagnostics:
Invalid formula type for gf_point.
Execution halted
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘magrittr’ ‘rpart’
All declared Imports should be used.
Version: 0.1.1
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘stringr’
All declared Imports should be used.
Version: 0.1.9
checking examples ... ERROR ``` Running examples in ‘stplanr-Ex.R’ failed The error most likely occurred in:
Name: geo_code
Title: Convert text strings into points on the map
Aliases: geo_code
** Examples
address = "LS7 3HB" geo_code(address = address) lon lat -1.534372 53.819472 geo_code(address = address, return_all = TRUE) Error: is.data.frame(x) is not TRUE Execution halted ```
Version: 1.6.0
...
summary.subsamples: no visible binding for global variable ‘o.padj’
summary.subsamples: no visible binding for global variable
‘significant’
summary.subsamples: no visible binding for global variable ‘estFDP’
summary.subsamples: no visible binding for global variable ‘rFDP’
summary.subsamples: no visible binding for global variable ‘metric’
summary.subsamples: no visible binding for global variable ‘value’
summary.subsamples: no visible binding for global variable ‘percent’
voomLimma: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
. ID average.depth average.value coefficient cor count cov depth
estFDP method metric model.matrix o.coefficient o.lfdr o.padj
p.adjust padj percent plot proportion pvalue rFDP rbinom replication
selectMethod significant valid value var
Consider adding
importFrom("graphics", "plot")
importFrom("methods", "selectMethod")
importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom",
"var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Version: 1.0.2
Package which this enhances but not available for checking: ‘treemap’
Version: 0.4.0
checking examples ... ERROR ``` ... LUNG no event 0.004340703 0.007643672 0.007643672 0.007643672 OV no event 0.004994699 0.007767270 0.008089927 0.008089927 BRCA death 0.003828336 0.005337151 0.005930541 0.005930541 LUNG death 0.006637210 0.007337434 0.007337434 0.007337434 OV death 0.004504398 0.005133510 0.005133510 0.005133510 BRCA progression 0.004378377 0.006110680 0.006110680 0.006110680 LUNG progression 0.006700958 0.008631668 0.009219678 0.009771658 OV progression 0.005033271 0.006681731 0.006681731 0.006681731
ggcompetingrisks(fit) ggcompetingrisks(fit, multiple_panels = FALSE) ggcompetingrisks(fit, conf.int = TRUE) ggcompetingrisks(fit, multiple_panels = FALSE, conf.int = TRUE)
handles survfitms objects
library(survival) df <- data.frame(time = ss, group = gg, status = cc, strt) fit2 <- survfit(Surv(time, status, type="mstate") ~ 1, data=df) ggcompetingrisks(fit2) Error: Aesthetics must be either length 1 or the same as the data (300): x, y, fill Execution halted ```
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 5.3Mb
Version: 0.2.0
Namespaces in Imports field not imported from:
‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
All declared Imports should be used.
Version: 1.0.0
Error in re-building vignettes:
...
Error: processing vignette 'swfdrTutorial.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
Version: 1.2.0
Found the following significant warnings:
Warning: replacing previous import ‘dplyr::exprs’ by ‘Biobase::exprs’ when loading ‘switchde’
See ‘/home/muelleki/git/R/dplyr/revdep/checks/switchde/new/switchde.Rcheck/00install.out’ for details.
checking re-building of vignette outputs ... WARNING ``` ... The following objects are masked from 'package:Biobase':
combine, exprs
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Warning: replacing previous import 'dplyr::exprs' by 'Biobase::exprs' when loading 'switchde' Warning: Removed 68 rows containing missing values (geom_path). Error: processing vignette 'switchde_vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
Version: 1.6.0
...
siRNAPlot: no visible global function definition for ‘pdf’
siRNAPlot: no visible global function definition for ‘dev.off’
tTest: no visible global function definition for ‘p.adjust’
zFactor: no visible binding for global variable ‘condition’
zFactor: no visible binding for global variable ‘sd’
zFactor: no visible binding for global variable ‘median’
zFactor: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
COL_NAME EXPERIMENT_MODIFICATION EXPERIMENT_TYPE MASTER_PLATE PLATE
READOUT ROW_NAME Var1 WELL_CONTENT_NAME colorRampPalette
complete.cases condition dev.off experiments is mad median medpolish
p.adjust pdf phyper rainbow sd siRNA t.test value write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
"rainbow")
importFrom("methods", "is")
importFrom("stats", "complete.cases", "mad", "median", "medpolish",
"p.adjust", "phyper", "sd", "t.test")
importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Version: 0.14.0
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘rmdformats’
checking data for non-ASCII characters ... NOTE
Note: found 3 marked UTF-8 strings
Version: 0.1.0
checking examples ... ERROR
...
4 data sets:
info:
# A tibble: 4 x 4
name n_legs dangerous taxon_id
<fctr> <dbl> <lgl> <chr>
1 cat 4 FALSE n
2 mole 4 FALSE o
3 tomato 0 FALSE q
# ... with 1 more rows
phylopic_ids: e148eabb-f138-43c6-b1e4-5cda2180485a ... 63604565-0406-460b-8cb8-1abe954b3f3a
foods: a list with 6 items
And 1 more data sets: abund
1 functions:
reaction
>
> # Remove taxa whose obserservation were filtered out
> filter_obs(ex_taxmap, "info", dangerous == FALSE, drop_taxa = TRUE)
Error in names(selection) <- self$taxon_ids() :
'names' attribute [17] must be the same length as the vector [2]
Calls: filter_obs ... filter_obs.Taxmap -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 317 SKIPPED: 0 FAILED: 31
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 258-259 (taxa-vignette.Rmd)
Error: processing vignette 'taxa-vignette.Rmd' failed with diagnostics:
'names' attribute [14] must be the same length as the vector [2]
Execution halted
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘knitr’ ‘lazyeval’ ‘rlang’
All declared Imports should be used.
Version: 0.1.4
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: > library(testthat) > test_check("taxizedb") Loading required package: taxizedb
testthat results ================================================================ OK: 59 SKIPPED: 0 FAILED: 1 1. Failure: db_load fails as expected - more (@test-db_load.R#33)
Error: testthat unit tests failed Execution halted ```
Version: 0.1.2
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
All declared Imports should be used.
Version: 2.5.9
checking examples ... ERROR
...
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
Error in checkProjectInput(project) :
Please set a valid project argument from the column id above. Project TCGA-ACC was not found.
Calls: GDCquery -> checkProjectInput
Execution halted
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 114 SKIPPED: 0 FAILED: 16
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ...
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 16-20 (clinical.Rmd) Error: processing vignette 'clinical.Rmd' failed with diagnostics: there is no package called 'DT' Execution halted ```
checking installed package size ... NOTE
installed size is 61.0Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 2.3Mb
doc 57.4Mb
checking R code for possible problems ... NOTE
...
‘limmacontrasts.fit’
TCGAanalyze_analyseGRN: no visible global function definition for
‘knnmi.cross’
TCGAanalyze_networkInference: no visible global function definition for
‘c3net’
TCGAanalyze_networkInference: no visible global function definition for
‘minet’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dNetInduce’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dNetPipeline’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dCommSignif’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘visNet’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
getTSS: no visible global function definition for ‘promoters’
Undefined global functions or variables:
c3net dCommSignif dNetInduce dNetPipeline knnmi.cross
limmacontrasts.fit limmamakeContrasts minet portions promoters value
visNet
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
Version: 2.2.1.11
checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 1.2Mb
doc 3.9Mb
libs 1.1Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘scales’
All declared Imports should be used.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'top.fun': ‘slice.fun’
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. ```
Version: 1.0.2
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
apps 2.6Mb
libs 2.1Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘data.table’ ‘datasets’ ‘stats’
All declared Imports should be used.
Version: 1.0.1
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 5.9Mb
Version: 0.1
Namespaces in Imports field not imported from:
‘nlme’ ‘tidyr’
All declared Imports should be used.
Version: 0.3
...
>
> # make up some data
> sim.data <- function() rpoilog(1000, 1.0, 1.0, condS=TRUE)
> otu <- data.frame(sample0=sim.data())
> for (i in 1:10) otu[[paste('sample', i, sep='')]] <- sim.data()
> otu.ids <- paste('otu', seq(1:1000), sep='')
> rownames(otu) <- otu.ids
> z.table <- z.transform.table(otu)
Warning in value[[3L]](cond) : fit 1 failed
Warning in value[[3L]](cond) : fit 1 failed
Warning in value[[3L]](cond) : fit 2 failed
>
> # pull out a quad, imagining that samples 1 and 2 were the control samples
> # and 3 and 4 were the treatment
> q <- quad.table(z.table, 'sample1', 'sample2', 'sample3', 'sample4')
>
> # plot it
> p <- quad.plot(q)
Error in get("d.control") : object 'd.control' not found
Calls: quad.plot ... map -> .Call -> .f -> overscope_eval_next -> .Call -> get
Execution halted
Version: 0.0.1
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/dplyr/revdep/checks/textmining/new/textmining.Rcheck/00install.out’ for details.
Version: 0.1.4
Package unavailable to check Rd xrefs: ‘tm’
Version: 1.0-8
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.2Mb
rda 3.8Mb
Version: 0.2.2
Version: 0.5.3
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 179 SKIPPED: 0 FAILED: 3 1. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#15) 2. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#17) 3. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#19)
Error: testthat unit tests failed In addition: Warning messages: 1: In download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' 2: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv'
Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv'
Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing AAPL. Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'FB', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing FB. Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'GOOG', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing GOOG. Warning in value[3L] : Returning as nested data frame. Quitting from lines 211-214 (TQ01-core-functions-in-tidyquant.Rmd) Error: processing vignette 'TQ01-core-functions-in-tidyquant.Rmd' failed with diagnostics: object 'Ask' not found Execution halted ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’
All declared Imports should be used.
Version: 0.7.2
Note: found 23 marked UTF-8 strings
Version: 1.2.2
Namespace in Imports field not imported from: ‘testthat’
All declared Imports should be used.
Version: 0.1.4
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: data argument must either be a dfmSparse (from quanteda) or a table with document and term columns 1: augment(stm_model, inaug) at testthat/test-stm-tidiers.R:57 2: augment.STM(stm_model, inaug) 3: stop("data argument must either be a dfmSparse ", "(from quanteda) or a table with document and term columns")
testthat results ================================================================ OK: 198 SKIPPED: 0 FAILED: 5 1. Error: Can cast tables into a sparse dfm (@test-sparse-casters.R#79) 2. Failure: Can tidy dfm from quanteda (@test-sparse-tidiers.R#34) 3. Failure: Can tidy dfm from quanteda (@test-sparse-tidiers.R#35) 4. Failure: Can tidy dfm from quanteda (@test-sparse-tidiers.R#36) 5. Error: can augment an stm output (@test-stm-tidiers.R#57)
Error: testthat unit tests failed Execution halted ```
Version: 1.2.1
Namespaces in Imports field not imported from:
‘dbplyr’ ‘reprex’ ‘rlang’
All declared Imports should be used.
Version: 0.2.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘sp’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 341 marked UTF-8 strings
Version: 0.3.1
Namespaces in Imports field not imported from:
‘devtools’ ‘forecast’
All declared Imports should be used.
Version: 0.1.1
Namespace in Imports field not imported from: ‘base’
All declared Imports should be used.
Version: 1.6.0
...
‘rainbow’
plotPrimordiumProfile: no visible binding for global variable ‘median’
plotPrimordiumProfile: no visible binding for global variable ‘mad’
plotPrimordiumProfile: no visible global function definition for ‘par’
plotPrimordiumProfile: no visible global function definition for ‘plot’
plotPrimordiumProfile: no visible global function definition for ‘axis’
plotPrimordiumProfile: no visible global function definition for
‘points’
plotPrimordiumProfile: no visible global function definition for
‘polygon’
plotPrimordiumProfile: no visible global function definition for ‘rgb’
simulatedRatio: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
approxfun axis mad median optimize par plot points polygon predict
rainbow rgb rnorm
Consider adding
importFrom("grDevices", "rainbow", "rgb")
importFrom("graphics", "axis", "par", "plot", "points", "polygon")
importFrom("stats", "approxfun", "mad", "median", "optimize",
"predict", "rnorm")
to your NAMESPACE file.
Version: 1.0.0
checking Rd \usage sections ... WARNING ``` Duplicated \argument entries in documentation object 'timescapeOutput': ‘width’ ‘height’ ‘mutations’ ‘height’ ‘width’ ‘clonal_prev’ ‘tree_edges’ ‘alpha’ ‘clonal_prev’ ‘tree_edges’ ‘genotype_position’ ‘clone_colours’ ‘perturbations’ ‘mutations’ ‘tree_edges’ ‘clonal_prev’ ‘clonal_prev’ ‘tree_edges’ ‘clone_colours’ ‘mutations’
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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
.vscode
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘dplyr’ ‘gtools’
All declared Imports should be used.
checking R code for possible problems ... NOTE
getMutationsData: no visible binding for global variable
‘show_warnings’
Undefined global functions or variables:
show_warnings
Version: 0.1.0
Namespaces in Imports field not imported from:
‘devtools’ ‘forecast’
All declared Imports should be used.
Version: 1.10
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 3.3Mb
Version: 0.1.0
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 48-52 (Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd) Error: processing vignette 'Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd' failed with diagnostics: 'roxygen2' >= 5.0.0 must be installed for this functionality. Execution halted ```
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘tidyr’
All declared Imports should be used.
Version: 3.4.3
checking examples ... ERROR
...
Removing duplicate identifiers using quality column 'qupm'...
261 out of 261 rows kept for further analysis.
Reformating data for input into function 'analyzeTPPCCR' ...
Done.
No output directory specified. No result files or plots will be produced.
Looking for intensity column prefix: 'sumionarea_protein_'
Computing fold changes...
Done.
Found the following column name in attr(data, 'importSettings')$proteinIdCol: 'representative'
Found the following column name in attr(data, 'importSettings')$fcStr: 'rel_fc_protein_'
Performing median normalization per temperature...
Done.
Looking for unique ID column: 'unique_ID'
Looking for nonZeroCols: 'qusm'
Checking which columns in the data table contain the fold change values for fitting and plotting...
Normalized data columns detected with prefix 'norm_rel_fc_protein_'. Analysis will be based on these values.
This information was found in the attributes of the input data (access with attr(dataTable, 'importSettings'))
Performing TPP-CCR dose response curve fitting and generating result table...
Error in foldChanges[, refCol] : incorrect number of dimensions
Calls: analyze2DTPP ... withCallingHandlers -> analyzeTPPCCR -> tppccrNormalizeToReference
Execution halted
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Calls: test_check ... -> lapply -> FUN -> cbind -> cbind -> data.frame testthat results ================================================================ OK: 130 SKIPPED: 0 FAILED: 9
Error: testthat unit tests failed Execution halted ```
checking whether package ‘TPP’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Biobase::exprs’ by ‘dplyr::exprs’ when loading ‘TPP’
See ‘/home/muelleki/git/R/dplyr/revdep/checks/TPP/new/TPP.Rcheck/00install.out’ for details.
checking re-building of vignette outputs ... WARNING ``` ...
Filtering by annotation column(s) 'qssm' in treatment group: Panobinostat_1 Column qssm between 4 and Inf-> 333 out of 508 proteins passed.
333 out of 508 proteins passed in total.
Filtering by annotation column(s) 'qssm' in treatment group: Panobinostat_2 Column qssm between 4 and Inf-> 364 out of 509 proteins passed.
364 out of 509 proteins passed in total.
2. Find jointP:
Detecting intersect between treatment groups (jointP). -> JointP contains 261 proteins.
3. Filtering fold changes:
Filtering fold changes in treatment group: Vehicle_1 Quitting from lines 73-76 (NPARC_analysis_of_TPP_TR_data.Rnw) Error: processing vignette 'NPARC_analysis_of_TPP_TR_data.Rnw' failed with diagnostics: incorrect number of dimensions Execution halted ```
checking installed package size ... NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
data 1.9Mb
example_data 8.0Mb
test_data 1.9Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘doParallel:::.options’ ‘mefa:::rep.data.frame’
See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ``` File ‘TPP/R/TPP.R’: .onLoad calls: packageStartupMessage(msgText, "\n")
See section ‘Good practice’ in '?.onAttach'.
plot_fSta_distribution: no visible binding for global variable ‘..density..’ plot_pVal_distribution: no visible binding for global variable ‘..density..’ Undefined global functions or variables: ..density.. ```
Version: 0.8-7
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
combn flush.console read.table
Consider adding
importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
Version: 0.9.0
Note: found 5 marked UTF-8 strings
Version: 0.2.0
Note: found 4494 marked UTF-8 strings
Version: 1.0.4
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
Version: 1.0.4
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
Version: 0.3.1
installed size is 15.5Mb
sub-directories of 1Mb or more:
libs 14.1Mb
Version: 1.5.0
installed size is 11.3Mb
sub-directories of 1Mb or more:
doc 3.0Mb
libs 7.5Mb
Version: 0.2.4
Namespaces in Imports field not imported from:
‘maptools’ ‘rgeos’
All declared Imports should be used.
Version: 4.7.0
Packages unavailable to check Rd xrefs: ‘mvoutlier’, ‘StatDA’, ‘mi’, ‘tkrplot’
Version: 1.2.0
Namespaces in Imports field not imported from:
‘iterators’ ‘knitr’ ‘testthat’
All declared Imports should be used.
Version: 3.44.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘hexbin’
All declared Imports should be used.
checking R code for possible problems ... NOTE
meanSdPlot,matrix: no visible binding for global variable ‘y’
Undefined global functions or variables:
y
Version: 0.1.0
Namespaces in Imports field not imported from:
‘lubridate’ ‘tibble’
All declared Imports should be used.
Version: 0.2.0
installed size is 46.9Mb
sub-directories of 1Mb or more:
libs 46.2Mb
Version: 0.6.4
Namespaces in Imports field not imported from:
‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘devtools’ ‘dismo’ ‘dplyr’ ‘maptools’
‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyBS’ ‘shinyjs’
‘shinythemes’ ‘spThin’ ‘spocc’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Version: 1.0.0
checking examples ... ERROR ``` ... The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationFilter
plotTranscriptsFromEnsembldb(EnsDb.Hsapiens.v86, "NCOA7", transcript_ids = c("ENST00000438495", "ENST00000392477")) Error in validObject(.Object) : invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class Calls: plotTranscriptsFromEnsembldb ... .AnnotationFilterList -> new -> initialize -> initialize -> validObject Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 148-152 (wiggleplotr.Rmd)
Error: processing vignette 'wiggleplotr.Rmd' failed with diagnostics:
invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class
Execution halted
Version: 1.1.1
checking whether package ‘windfarmGA’ can be installed ... WARNING
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/dplyr/revdep/checks/windfarmGA/new/windfarmGA.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RandomFields’
All declared Imports should be used.
Version: 0.2.0
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 27-31 (wordbankr.Rmd)
Error: processing vignette 'wordbankr.Rmd' failed with diagnostics:
Condition message must be a string
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RMySQL’
All declared Imports should be used.
Version: 1.0-1
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... Quitting from lines 622-635 (wrswoR.Rmd) Error: processing vignette 'wrswoR.Rmd' failed with diagnostics:
TeX was unable to calculate metrics for the following string or character:
77
Common reasons for failure include: * The string contains a character which is special to LaTeX unless escaped properly, such as % or $. * The string makes use of LaTeX commands provided by a package and the tikzDevice was not told to load the package.
The contents of the LaTeX log of the aborted run have been printed above, it may contain additional details as to why the metric calculation failed. Execution halted ```
Version: 1.6.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Welcome to 'XBSeq'.
test_check("XBSeq") estimating parameters using MLE for group one estimating parameters using MLE for group two Error: XBplot(XB, Samplenum = "Sample_54_WT") did not throw an error. testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Attaching package: 'DESeq'
The following object is masked from 'package:XBSeq':
fitInfo
The following objects are masked from 'package:DESeq2':
estimateSizeFactorsForMatrix, getVarianceStabilizedData,
varianceStabilizingTransformation
Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'
Warning: Transformation introduced infinite values in continuous x-axis Warning: Removed 17 rows containing missing values (geom_point). Warning: Removed 2 rows containing missing values (geom_point). Error: processing vignette 'XBSeq.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘XBSeq’ for: ‘conditions’, ‘conditions<-’, ‘dispTable’
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 R code for possible problems ... NOTE
...
estimateRealCount,XBSeqDataSet: no visible global function definition
for ‘assay’
estimateRealCount,XBSeqDataSet: no visible global function definition
for ‘assay<-’
estimateSCV,XBSeqDataSet: no visible global function definition for
‘conditions’
estimateSCV,XBSeqDataSet: no visible global function definition for
‘dispTable<-’
Undefined global functions or variables:
..count.. DataFrame Gamma Group Sample SummarizedExperiment assay
assay<- assays baseMean coefficients complete.cases conditions cor
data ddelap dispTable dispTable<- dnbinom dpois formula glm
log2FoldChange median optim p.adjust pbeta predict qbeta quantile
rnbinom scvBiasCorrectionFits
Consider adding
importFrom("stats", "Gamma", "coefficients", "complete.cases", "cor",
"dnbinom", "dpois", "formula", "glm", "median", "optim",
"p.adjust", "pbeta", "predict", "qbeta", "quantile",
"rnbinom")
importFrom("utils", "data")
to your NAMESPACE file.
Version: 0.1.0
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
Version: 2.0.3
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
Version: 0.1.1
Namespaces in Imports field not imported from:
‘Amelia’ ‘MatchIt’ ‘WhatIf’
All declared Imports should be used.
Version: 0.1.7
Namespace in Imports field not imported from: ‘rootSolve’
All declared Imports should be used.
Version: 0.1.0
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘lubridate’
All declared Imports should be used.
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