Run revdep_details(, "BasketballAnalyzeR")
for more info
Namespaces in Imports field not imported from:
‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
All declared Imports should be used.
Run revdep_details(, "BGGM")
for more info
installed size is 12.8Mb
sub-directories of 1Mb or more:
doc 3.8Mb
help 1.1Mb
libs 7.2Mb
Run revdep_details(, "bingat")
for more info
Package unavailable to check Rd xrefs: ‘genalg’
Run revdep_details(, "Blaunet")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgets2tcltk’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "bootcluster")
for more info
Namespace in Imports field not imported from: ‘sna’
All declared Imports should be used.
Run revdep_details(, "broom")
for more info
checking package dependencies ... NOTE
Packages suggested but not available for checking:
'epiR', 'spdep', 'spatialreg'
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘spatialreg’, ‘epiR’
Run revdep_details(, "CEMiTool")
for more info
checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 3.1Mb
doc 2.3Mb
extdata 2.8Mb
checking R code for possible problems ... NOTE
flip_vector: no visible global function definition for ‘setNames’
select_genes: no visible global function definition for ‘var’
get_hubs,CEMiTool : <anonymous>: no visible global function definition
for ‘head’
get_merged_mods,CEMiTool: no visible global function definition for
‘as.dist’
get_mods,CEMiTool: no visible global function definition for ‘as.dist’
get_phi,CEMiTool: no visible global function definition for ‘tail’
get_phi,CEMiTool: no visible global function definition for ‘head’
mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’
...
save_plots,CEMiTool: no visible global function definition for
‘dev.off’
Undefined global functions or variables:
..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist
head modules num_genes setNames tail var
Consider adding
importFrom("grDevices", "dev.off")
importFrom("stats", "as.dist", "dist", "setNames", "var")
importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Run revdep_details(, "CeTF")
for more info
checking re-building of vignette outputs ...sh: line 1: 247279 Killed '/srv/scratch/z3528859/R-4.2.0/bin/R' --vanilla --no-echo > '/srv/scratch/z3528859/github/statnet/network/revdep/checks/CeTF/old/CeTF.Rcheck/build_vignettes.log' 2>&1 < '/scratch/pbs.3584821.kman.restech.unsw.edu.au/Rtmp5JkIUj/file375426c1496a9' ``` ERROR Error(s) in re-building vignettes: --- re-building ‘CeTF.Rmd’ using rmarkdown
======================================== CeTF version 1.8.0 Bioconductor page: http://bioconductor.org/packages/CeTF/ Github page: https://github.com/cbiagii/CeTF or https://cbiagii.github.io/CeTF/ Documentation: http://bioconductor.org/packages/CeTF/ If you use it in published research, please cite: ... count
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
```
installed size is 7.6Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 3.0Mb
libs 2.5Mb
Run revdep_details(, "chorrrds")
for more info
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘forcats’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 4004 marked UTF-8 strings
Run revdep_details(, "CINNA")
for more info
Namespace in Imports field not imported from: ‘circlize’
All declared Imports should be used.
Run revdep_details(, "CluMSID")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘MSnbase’
Packages suggested but not available for checking: 'metaMS', 'xcms'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "conserveR")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘scales’ ‘sna’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 244 marked UTF-8 strings
Run revdep_details(, "edgebundle")
for more info
Note: found 22 marked UTF-8 strings
Run revdep_details(, "ergm")
for more info
installed size is 8.3Mb
sub-directories of 1Mb or more:
R 1.1Mb
doc 1.7Mb
libs 3.8Mb
Run revdep_details(, "ergMargins")
for more info
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘methods’ ‘sna’ ‘statnet.common’
All declared Imports should be used.
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘margins’
Run revdep_details(, "ergmito")
for more info
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 5.7Mb
Run revdep_details(, "fcoex")
for more info
checking examples ... ERROR ``` Running examples in ‘fcoex-Ex.R’ failed The error most likely occurred in:
Name: mod_ora
Title: Over Representation Analysis (ORA)
Aliases: mod_ora mod_ora,fcoex-method
** Examples
data("fc") ... gmt_fname <- system.file("extdata", "pathways.gmt", package = "CEMiTool") gmt_in <- pathwayPCA::read_gmt(gmt_fname) Warning in file(con, "rb") : file("") only supports open = "w+" and open = "w+b": using the former Warning in readChar(file, nchars = nChars, useBytes = TRUE) : text connection used with readChar(), results may be incorrect Error in readChar(file, nchars = nChars, useBytes = TRUE) : invalid 'nchars' argument Calls: -> readChar Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘fcoex.Rmd’ using rmarkdown
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
... Quitting from lines 67-75 (fcoex_and_seurat.Rmd) Error: processing vignette 'fcoex_and_seurat.Rmd' failed with diagnostics: invalid 'nchars' argument --- failed re-building ‘fcoex_and_seurat.Rmd’
SUMMARY: processing the following files failed: ‘fcoex.Rmd’ ‘fcoex_and_seurat.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking whether package ‘fcoex’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’
See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/fcoex/new/fcoex.Rcheck/00install.out’ for details.
checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object '.plot_one_interaction': ‘...’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE
Packages suggested but not available for checking: 'TENxPBMCData', 'schex'
Run revdep_details(, "fssemR")
for more info
checking installed package size ... NOTE
installed size is 15.2Mb
sub-directories of 1Mb or more:
libs 14.5Mb
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘qpdf’
All declared Imports should be used.
Run revdep_details(, "geomnet")
for more info
checking examples ... ERROR ``` Running examples in ‘geomnet-Ex.R’ failed The error most likely occurred in:
Name: football
Title: College football games network (undirected)
Aliases: football
Keywords: datasets
** Examples
... + scale_colour_brewer("Conference", palette = "Paired") Error:
loops
isFALSE
, butx
contains loops. The following values are affected: -x[604, 1:2]
-x[605, 1:2]
-x[610, 1:2]
-x[615, 1:2]
-x[617, 1:2]
-x[618, 1:2]
Execution halted ```
checking re-building of vignette outputs ... ERROR
``
Error(s) in re-building vignettes:
...
--- re-building ‘geomnet-vignette.Rmd’ using rmarkdown
Quitting from lines 15-112 (geomnet-vignette.Rmd)
Error: processing vignette 'geomnet-vignette.Rmd' failed with diagnostics:
The first two columns of
x` must be of the same type.
--- failed re-building ‘geomnet-vignette.Rmd’
SUMMARY: processing the following file failed: ‘geomnet-vignette.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdep_details(, "GGally")
for more info
Package suggested but not available for checking: ‘scagnostics’
Run revdep_details(, "GGMncv")
for more info
Namespaces in Imports field not imported from:
‘Rdpack’ ‘mathjaxr’
All declared Imports should be used.
Run revdep_details(, "GGMnonreg")
for more info
Namespaces in Imports field not imported from:
‘Matrix’ ‘Rdpack’
All declared Imports should be used.
Run revdep_details(, "ggnetwork")
for more info
Namespaces in Imports field not imported from:
‘sna’ ‘utils’
All declared Imports should be used.
Run revdep_details(, "GGPA")
for more info
checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
doc 1.6Mb
libs 3.9Mb
checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘network’ ‘scales’ ‘sna’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking compiled code ... NOTE ``` File ‘GGPA/libs/GGPA.so’: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘3_Param.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "ggraph")
for more info
installed size is 8.9Mb
sub-directories of 1Mb or more:
doc 3.6Mb
libs 4.0Mb
Run revdep_details(, "GOxploreR")
for more info
installed size is 6.7Mb
sub-directories of 1Mb or more:
R 6.1Mb
Run revdep_details(, "GRENITS")
for more info
checking installed package size ... NOTE
installed size is 10.9Mb
sub-directories of 1Mb or more:
libs 10.6Mb
checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE
.heatMap.ggplot: no visible global function definition for ‘ggplot’
.heatMap.ggplot: no visible global function definition for ‘aes’
.heatMap.ggplot: no visible binding for global variable ‘Var2’
.heatMap.ggplot: no visible binding for global variable ‘Var1’
.heatMap.ggplot: no visible global function definition for ‘geom_tile’
.heatMap.ggplot: no visible binding for global variable ‘value’
.heatMap.ggplot: no visible global function definition for
‘scale_fill_gradient’
.heatMap.ggplot: no visible global function definition for ‘theme’
.heatMap.ggplot: no visible global function definition for
...
.plotDistribParents.LargeMat: no visible global function definition for
‘scale_x_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
‘scale_y_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
‘facet_wrap’
Undefined global functions or variables:
GeneNames Var1 Var2 aes element_blank element_text facet_wrap
geom_tile ggplot ggtitle labs scale_fill_gradient scale_x_discrete
scale_y_discrete theme value variable
Run revdep_details(, "gwdegree")
for more info
checking R code for possible problems ... NOTE
simCCCent : <anonymous>: no visible global function definition for
‘simulate.formula’
Undefined global functions or variables:
simulate.formula
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "ICON")
for more info
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On CRAN (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-s3-network.R:21:3): as.network.ICON generic works ─────────────
network::get.edge.attribute(converted_network, "attrib") not equal to test_obj$attrib.
Lengths differ: 21 is not 25
── Failure (test-s3-network.R:24:3): as.network.ICON generic works ─────────────
network::network.edgecount(converted_network) not equal to NROW
.
1/1 mismatches
[1] 21 - 25 == -4
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ] Error: Test failures Execution halted ```
Run revdep_details(, "InflectSSP")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘xlsx’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "latentnet")
for more info
GNU make is a SystemRequirements.
Run revdep_details(, "leiden")
for more info
checking tests ... ``` Running ‘spelling.R’ Running ‘testthat.R’/srv/scratch/z3528859/R-4.2.0/bin/BATCH: line 60: 67256 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output:
library("testthat") library("leiden") Unable to set up conda environment r-reticulate run in terminal: conda init conda create -n r-reticulate conda environment r-reticulate installed Unable to install python modules igraph and leidenalg run in terminal: conda install -n r-reticulate -c conda-forge vtraag python-igraph pandas umap learn python modules igraph and leidenalg installed
test_check("leiden") ```
installed size is 6.0Mb
sub-directories of 1Mb or more:
doc 5.9Mb
Run revdep_details(, "lolog")
for more info
R CMD check timed out
checking installed package size ... NOTE
installed size is 24.8Mb
sub-directories of 1Mb or more:
libs 23.1Mb
Run revdep_details(, "MBCbook")
for more info
Note: found 66 marked UTF-8 strings
Run revdep_details(, "migraph")
for more info
checking tests ...
``
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-viz_autographr.R:115:3): fancy node mods graph correctly ──────
class(testcolnodes) not equal to c("ggraph", "gg", "ggplot").
Lengths differ: 1 is not 3
── Error (test-viz_autographr.R:116:3): fancy node mods graph correctly ────────
Error in
round(testcolnodes$data$x[1])`: non-numeric argument to mathematical function
Backtrace:
▆
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 526 ] Error: Test failures Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘concaveman’
checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
doc 3.0Mb
Run revdep_details(, "mpa")
for more info
checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ``` NB: .First.lib is obsolete and will not be used in R >= 3.0.0 File ‘mpa/R/zzz.R’: .First.lib calls: cat("\n mpa: CoWords Method") cat("\n ") cat("\n Universidad Nacional de Colombia") cat("\n ") cat("\n Elaborado por: Daniel Rodriguez dhrodriguezt@unal.edu.co") cat("\n Campo Elias Pardo cepardot@unal.edu.co") cat("\n For help: ?mpa \n\n") ... generate messages. See section ‘Good practice’ in '?.onAttach'.
diagram.mpa: no visible global function definition for ‘abline’ diagram.mpa: no visible global function definition for ‘text’ Undefined global functions or variables: abline text Consider adding importFrom("graphics", "abline", "text") to your NAMESPACE file. ```
checking data for non-ASCII characters ... NOTE
Note: found 6 marked UTF-8 strings
Run revdep_details(, "netdiffuseR")
for more info
installed size is 13.2Mb
sub-directories of 1Mb or more:
doc 2.5Mb
libs 8.8Mb
Run revdep_details(, "nethet")
for more info
checking whether package ‘nethet’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/nethet/new/nethet.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE
screen_shrink: no visible global function definition for
‘performance.pcor’
Undefined global functions or variables:
performance.pcor
Run revdep_details(, "netmap")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘sf’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "netmediate")
for more info
Package unavailable to check Rd xrefs: ‘mediation’
Run revdep_details(, "networksis")
for more info
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
var
Consider adding
importFrom("stats", "var")
to your NAMESPACE file.
Run revdep_details(, "PDN")
for more info
Namespace in Imports field not imported from: ‘glmnet’
All declared Imports should be used.
Run revdep_details(, "PhosR")
for more info
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 3.3Mb
doc 2.2Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’
‘SummarizedExperiment:::.SummarizedExperiment.charbound’
See the note in ?`:::` about the use of this operator.
Run revdep_details(, "predictionet")
for more info
checking whether package ‘predictionet’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'predictionet' is deprecated and will be removed from
See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/predictionet/new/predictionet.Rcheck/00install.out’ for details.
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘catnet’ ‘igraph’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE
.build.regression.regrnet: no visible global function definition for
‘formula’
.build.regression.regrnet: no visible global function definition for
‘lm’
.build2.mim: no visible global function definition for ‘cor’
.exportGML: no visible global function definition for ‘vcount’
.exportGML: no visible global function definition for ‘ecount’
.get.ii4triplets.gaussian: no visible global function definition for
‘cor’
.pred.onegene.bayesnet.fs : <anonymous>: no visible global function
...
Undefined global functions or variables:
as cnMatParents coefficients complete.cases cor ecount formula lm
quantile sessionInfo vcount
Consider adding
importFrom("methods", "as")
importFrom("stats", "coefficients", "complete.cases", "cor", "formula",
"lm", "quantile")
importFrom("utils", "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking compiled code ... NOTE ``` File ‘predictionet/libs/predictionet.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘mrnet_ensemble_standalone.o’ Found ‘srand’, possibly from ‘srand’ (C) Object: ‘mrnet_ensemble_standalone.o’
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "PubScore")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘PubScore_vignette.Rmd’ using rmarkdown Quitting from lines 144-153 (PubScore_vignette.Rmd) Error: processing vignette 'PubScore_vignette.Rmd' failed with diagnostics: Gateway Timeout (HTTP 504). --- failed re-building ‘PubScore_vignette.Rmd’
SUMMARY: processing the following file failed: ‘PubScore_vignette.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking whether package ‘PubScore’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'PubScore' is deprecated and will be removed from Bioconductor
See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/PubScore/new/PubScore.Rcheck/00install.out’ for details.
checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
data 4.2Mb
doc 4.9Mb
checking R code for possible problems ... NOTE
get_literature_score: no visible binding for global variable
‘gene2pubmed_db’
get_literature_score: no visible binding for global variable
‘hgcn_entrez_reference’
get_sum_of_weights: no visible binding for global variable ‘Genes’
get_sum_of_weights: no visible binding for global variable ‘Topic’
plot_literature_score: no visible binding for global variable ‘Genes’
plot_literature_score: no visible binding for global variable ‘Topic’
plot_literature_score: no visible binding for global variable
‘number_of_articles’
show,PubScore: no visible binding for global variable ‘pub’
Undefined global functions or variables:
Genes Topic gene2pubmed_db hgcn_entrez_reference number_of_articles
pub
Run revdep_details(, "RSiena")
for more info
installed size is 19.1Mb
sub-directories of 1Mb or more:
R 1.0Mb
libs 17.2Mb
Run revdep_details(, "sand")
for more info
Note: found 6 marked UTF-8 strings
Run revdep_details(, "SBICgraph")
for more info
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘network’
All declared Imports should be used.
checking LazyData ... NOTE
'LazyData' is specified without a 'data' directory
Run revdep_details(, "sparsebnUtils")
for more info
Unknown package ‘sparsebn’ in Rd xrefs
Run revdep_details(, "statnetWeb")
for more info
'LazyData' is specified without a 'data' directory
Run revdep_details(, "vivid")
for more info
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘zenplots’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘RColorBrewer’ ‘colorspace’ ‘tidyr’
All declared Imports should be used.
Run revdep_details(, "wildlifeDI")
for more info
checking package dependencies ... ERROR ``` Package required but not available: ‘sf’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Run revdep_details(, "WOTPLY")
for more info
Namespace in Imports field not imported from: ‘sna’
All declared Imports should be used.
Run revdep_details(, "xergm.common")
for more info
Package unavailable to check Rd xrefs: ‘RSiena’
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