lconway Summary
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| Package: multiWGCNA |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data multiWGCNA |
| BuildTime: 2 minutes 26.98 seconds |
| CheckCommand: BiocCheckGitClone('multiWGCNA') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3063/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.install-out.txt multiWGCNA_0.99.1.tar.gz && BiocCheck('multiWGCNA_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 6.84 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh multiWGCNA_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 20.70 seconds |
| PackageFileSize: 2008.92 KiB |
| BuildID:: multiWGCNA_20230706154111 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: multiWGCNA. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* preparing ‘multiWGCNA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘multiWGCNA_0.99.1.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('multiWGCNA')
===============================
─ BiocCheckVersion: 1.37.5
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiWGCNA’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘multiWGCNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [21s/21s] NOTE
bidirectionalBestMatches: no visible binding for global variable ‘mod1’
bidirectionalBestMatches: no visible binding for global variable ‘mod2’
bidirectionalBestMatches: no visible binding for global variable
‘overlap’
coexpressionLineGraph: no visible binding for global variable ‘Var1’
coexpressionLineGraph: no visible binding for global variable ‘value’
coexpressionLineGraph: no visible binding for global variable ‘Var2’
computeOverlapsFromWGCNA: no visible global function definition for
‘phyper’
computeOverlapsFromWGCNA: no visible global function definition for
‘p.adjust’
computeOverlapsFromWGCNA: no visible binding for global variable ‘mod1’
computeOverlapsFromWGCNA: no visible binding for global variable ‘mod2’
continuousFlowPlot: no visible global function definition for ‘ulist’
continuousFlowPlot: no visible global function definition for ‘head’
continuousFlowPlot: no visible binding for global variable
‘uniqueSortedData’
continuousFlowPlot: no visible binding for global variable ‘stratum’
continuousFlowPlot: no visible global function definition for ‘error’
correlationComparisonBoxplot: no visible global function definition for
‘t.test’
correlationComparisonBoxplot: no visible binding for global variable
‘Status’
correlationComparisonBoxplot: no visible binding for global variable
‘Correlation’
correlationComparisonHeatmaps: no visible binding for global variable
‘Var1’
correlationComparisonHeatmaps: no visible binding for global variable
‘Var2’
correlationComparisonHeatmaps: no visible binding for global variable
‘value’
diffCoexpression: no visible binding for global variable ‘p.adjust’
diffCoexpression: no visible global function definition for ‘na.omit’
diffCoexpression : <anonymous>: no visible global function definition
for ‘rgb’
diffCoexpression: no visible global function definition for ‘rgb’
diffCoexpression: no visible binding for global variable
‘layout_with_fr’
diffCoexpression: no visible binding for global variable ‘p.adj’
diffModuleExpression: no visible binding for global variable ‘sd’
diffModuleExpression: no visible global function definition for
‘na.omit’
diffModuleExpression: no visible binding for global variable ‘Sample’
drawMultiWGCNAnetwork: no visible global function definition for
‘runif’
drawMultiWGCNAnetwork : <anonymous>: no visible global function
definition for ‘rgb’
drawMultiWGCNAnetwork: no visible global function definition for
‘legend’
drawNetwork: no visible binding for global variable ‘layout_with_fr’
drawNetwork : <anonymous>: no visible global function definition for
‘rgb’
expressionHeatmap: no visible global function definition for ‘na.omit’
expressionHeatmap: no visible binding for global variable ‘sd’
expressionHeatmap: no visible global function definition for ‘dist’
expressionHeatmap: no visible binding for global variable ‘Sample’
expressionHeatmap: no visible binding for global variable ‘Gene’
expressionHeatmap: no visible binding for global variable ‘Zscore’
findModuleEigengenes: no visible global function definition for
‘write.csv’
findOutlierModules: no visible global function definition for
‘zScoreMatrix’
findOutlierModules : <anonymous>: no visible global function definition
for ‘quantile’
findOutlierModules : <anonymous>: no visible global function definition
for ‘IQR’
findOutlierModules : <anonymous>: no visible global function definition
for ‘var’
getPreservation: no visible global function definition for ‘write.csv’
moduleComparisonPlot: no visible binding for global variable ‘overlap’
moduleComparisonPlot: no visible binding for global variable ‘mod1’
moduleComparisonPlot: no visible binding for global variable ‘mod2’
moduleComparisonPlot: no visible binding for global variable ‘p.adj’
moduleComparisonPlot: no visible binding for global variable ‘stratum’
moduleExpressionPlot: no visible binding for global variable ‘sd’
moduleExpressionPlot: no visible global function definition for
‘na.omit’
moduleExpressionPlot: no visible binding for global variable ‘Sample’
moduleExpressionPlot: no visible binding for global variable
‘Expression’
moduleToModuleHeatmap: no visible binding for global variable ‘mod1’
moduleToModuleHeatmap: no visible binding for global variable ‘mod2’
moduleToModuleHeatmap: no visible binding for global variable ‘p.adj’
moduleToModuleHeatmap: no visible binding for global variable ‘overlap’
overlapComparisons: no visible global function definition for
‘write.csv’
performANOVA: no visible global function definition for ‘lm’
performANOVA: no visible global function definition for ‘anova’
performWGCNA: no visible global function definition for ‘write.csv’
plotModules: no visible global function definition for ‘pdf’
plotModules: no visible global function definition for ‘dev.off’
preservationComparisonPlot: no visible binding for global variable
‘log10Pvalue’
preservationComparisonPlot: no visible binding for global variable
‘Zsum’
preservationComparisonPlot: no visible binding for global variable
‘trait’
preservationComparisonPlot: no visible binding for global variable
‘Module’
printModules: no visible global function definition for ‘write.table’
runDME: no visible global function definition for ‘pdf’
runDME: no visible global function definition for ‘dev.off’
summarizeResults: no visible global function definition for
‘capture.output’
topNGenes: no visible binding for global variable ‘kWithin’
topNGenes: no visible global function definition for ‘head’
traitCor: no visible global function definition for ‘write.csv’
show,WGCNA: no visible global function definition for ‘head’
Undefined global functions or variables:
Correlation Expression Gene IQR Module Sample Status Var1 Var2 Zscore
Zsum anova capture.output dev.off dist error head kWithin
layout_with_fr legend lm log10Pvalue mod1 mod2 na.omit overlap p.adj
p.adjust pdf phyper quantile rgb runif sd stratum t.test trait ulist
uniqueSortedData value var write.csv write.table zScoreMatrix
Consider adding
importFrom("grDevices", "dev.off", "pdf", "rgb")
importFrom("graphics", "legend")
importFrom("stats", "IQR", "anova", "dist", "lm", "na.omit",
"p.adjust", "phyper", "quantile", "runif", "sd", "t.test",
"var")
importFrom("utils", "capture.output", "head", "write.csv",
"write.table")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [344s/413s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
preservationComparisonPlot 46.498 3.690 52.341
constructNetworks 45.018 1.564 48.628
preservationComparisons 43.117 3.153 52.098
drawMultiWGCNAnetwork 18.764 2.329 25.358
runDME 18.272 1.775 24.351
diffModuleExpression 16.898 2.585 23.629
moduleComparisonPlot 16.449 1.942 27.116
iterate 11.842 2.298 16.303
bidirectionalBestMatches 12.012 1.929 24.179
overlapComparisons 10.849 1.048 14.129
moduleToModuleHeatmap 9.163 0.899 12.681
moduleExpressionPlot 8.868 1.134 12.242
computeOverlapsFromWGCNA 8.713 1.233 12.169
cleanDatExpr 7.722 1.561 11.599
name 8.088 0.969 11.250
diffCoexpression 7.700 1.266 17.468
topNGenes 7.847 1.064 11.093
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.Rcheck/00check.log’
for details.
===============================
BiocCheck('multiWGCNA_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.5
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpvNIdBG/file37232c8c05ec/multiWGCNA
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpvNIdBG/file3723624d1a86
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of multiWGCNA...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 296 lines (9%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 947 lines (29%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 289 lines
(9%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 10 NOTES
See the multiWGCNA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir multiWGCNA_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘multiWGCNA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (multiWGCNA)
nebbiolo2 Summary
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| Package: multiWGCNA |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data multiWGCNA |
| BuildTime: 3 minutes 13.23 seconds |
| CheckCommand: BiocCheckGitClone('multiWGCNA') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3063/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.install-out.txt multiWGCNA_0.99.1.tar.gz && BiocCheck('multiWGCNA_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 7 minutes 54.96 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1859.79 KiB |
| BuildID:: multiWGCNA_20230706154111 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: multiWGCNA. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* preparing ‘multiWGCNA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘multiWGCNA_0.99.1.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('multiWGCNA')
===============================
─ BiocCheckVersion: 1.37.5
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiWGCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiWGCNA’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘multiWGCNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [32s/32s] NOTE
bidirectionalBestMatches: no visible binding for global variable ‘mod1’
bidirectionalBestMatches: no visible binding for global variable ‘mod2’
bidirectionalBestMatches: no visible binding for global variable
‘overlap’
coexpressionLineGraph: no visible binding for global variable ‘Var1’
coexpressionLineGraph: no visible binding for global variable ‘value’
coexpressionLineGraph: no visible binding for global variable ‘Var2’
computeOverlapsFromWGCNA: no visible global function definition for
‘phyper’
computeOverlapsFromWGCNA: no visible global function definition for
‘p.adjust’
computeOverlapsFromWGCNA: no visible binding for global variable ‘mod1’
computeOverlapsFromWGCNA: no visible binding for global variable ‘mod2’
continuousFlowPlot: no visible global function definition for ‘ulist’
continuousFlowPlot: no visible global function definition for ‘head’
continuousFlowPlot: no visible binding for global variable
‘uniqueSortedData’
continuousFlowPlot: no visible binding for global variable ‘stratum’
continuousFlowPlot: no visible global function definition for ‘error’
correlationComparisonBoxplot: no visible global function definition for
‘t.test’
correlationComparisonBoxplot: no visible binding for global variable
‘Status’
correlationComparisonBoxplot: no visible binding for global variable
‘Correlation’
correlationComparisonHeatmaps: no visible binding for global variable
‘Var1’
correlationComparisonHeatmaps: no visible binding for global variable
‘Var2’
correlationComparisonHeatmaps: no visible binding for global variable
‘value’
diffCoexpression: no visible binding for global variable ‘p.adjust’
diffCoexpression: no visible global function definition for ‘na.omit’
diffCoexpression : <anonymous>: no visible global function definition
for ‘rgb’
diffCoexpression: no visible global function definition for ‘rgb’
diffCoexpression: no visible binding for global variable
‘layout_with_fr’
diffCoexpression: no visible binding for global variable ‘p.adj’
diffModuleExpression: no visible binding for global variable ‘sd’
diffModuleExpression: no visible global function definition for
‘na.omit’
diffModuleExpression: no visible binding for global variable ‘Sample’
drawMultiWGCNAnetwork: no visible global function definition for
‘runif’
drawMultiWGCNAnetwork : <anonymous>: no visible global function
definition for ‘rgb’
drawMultiWGCNAnetwork: no visible global function definition for
‘legend’
drawNetwork: no visible binding for global variable ‘layout_with_fr’
drawNetwork : <anonymous>: no visible global function definition for
‘rgb’
expressionHeatmap: no visible global function definition for ‘na.omit’
expressionHeatmap: no visible binding for global variable ‘sd’
expressionHeatmap: no visible global function definition for ‘dist’
expressionHeatmap: no visible binding for global variable ‘Sample’
expressionHeatmap: no visible binding for global variable ‘Gene’
expressionHeatmap: no visible binding for global variable ‘Zscore’
findModuleEigengenes: no visible global function definition for
‘write.csv’
findOutlierModules: no visible global function definition for
‘zScoreMatrix’
findOutlierModules : <anonymous>: no visible global function definition
for ‘quantile’
findOutlierModules : <anonymous>: no visible global function definition
for ‘IQR’
findOutlierModules : <anonymous>: no visible global function definition
for ‘var’
getPreservation: no visible global function definition for ‘write.csv’
moduleComparisonPlot: no visible binding for global variable ‘overlap’
moduleComparisonPlot: no visible binding for global variable ‘mod1’
moduleComparisonPlot: no visible binding for global variable ‘mod2’
moduleComparisonPlot: no visible binding for global variable ‘p.adj’
moduleComparisonPlot: no visible binding for global variable ‘stratum’
moduleExpressionPlot: no visible binding for global variable ‘sd’
moduleExpressionPlot: no visible global function definition for
‘na.omit’
moduleExpressionPlot: no visible binding for global variable ‘Sample’
moduleExpressionPlot: no visible binding for global variable
‘Expression’
moduleToModuleHeatmap: no visible binding for global variable ‘mod1’
moduleToModuleHeatmap: no visible binding for global variable ‘mod2’
moduleToModuleHeatmap: no visible binding for global variable ‘p.adj’
moduleToModuleHeatmap: no visible binding for global variable ‘overlap’
overlapComparisons: no visible global function definition for
‘write.csv’
performANOVA: no visible global function definition for ‘lm’
performANOVA: no visible global function definition for ‘anova’
performWGCNA: no visible global function definition for ‘write.csv’
plotModules: no visible global function definition for ‘pdf’
plotModules: no visible global function definition for ‘dev.off’
preservationComparisonPlot: no visible binding for global variable
‘log10Pvalue’
preservationComparisonPlot: no visible binding for global variable
‘Zsum’
preservationComparisonPlot: no visible binding for global variable
‘trait’
preservationComparisonPlot: no visible binding for global variable
‘Module’
printModules: no visible global function definition for ‘write.table’
runDME: no visible global function definition for ‘pdf’
runDME: no visible global function definition for ‘dev.off’
summarizeResults: no visible global function definition for
‘capture.output’
topNGenes: no visible binding for global variable ‘kWithin’
topNGenes: no visible global function definition for ‘head’
traitCor: no visible global function definition for ‘write.csv’
show,WGCNA: no visible global function definition for ‘head’
Undefined global functions or variables:
Correlation Expression Gene IQR Module Sample Status Var1 Var2 Zscore
Zsum anova capture.output dev.off dist error head kWithin
layout_with_fr legend lm log10Pvalue mod1 mod2 na.omit overlap p.adj
p.adjust pdf phyper quantile rgb runif sd stratum t.test trait ulist
uniqueSortedData value var write.csv write.table zScoreMatrix
Consider adding
importFrom("grDevices", "dev.off", "pdf", "rgb")
importFrom("graphics", "legend")
importFrom("stats", "IQR", "anova", "dist", "lm", "na.omit",
"p.adjust", "phyper", "quantile", "runif", "sd", "t.test",
"var")
importFrom("utils", "capture.output", "head", "write.csv",
"write.table")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [281s/287s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
preservationComparisonPlot 56.033 0.668 56.951
preservationComparisons 51.938 0.880 53.151
constructNetworks 52.374 0.324 52.866
moduleComparisonPlot 16.003 0.276 16.574
runDME 10.233 0.356 10.975
drawMultiWGCNAnetwork 10.365 0.120 10.879
iterate 8.332 0.464 9.117
overlapComparisons 7.761 0.080 8.124
diffModuleExpression 7.364 0.104 7.877
bidirectionalBestMatches 6.702 0.371 8.390
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.Rcheck/00check.log’
for details.
===============================
BiocCheck('multiWGCNA_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.5
─ BiocVersion: 3.18
─ Package: multiWGCNA
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpAIlnHE/file5aa021b62240b/multiWGCNA
─ installDir: /tmp/RtmpAIlnHE/file5aa0210b79d4b
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3063/7d0097c1083e53afb84c6256083c4e198ab80ca1/multiWGCNA.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of multiWGCNA...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 296 lines (9%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 947 lines (29%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 289 lines
(9%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 10 NOTES
See the multiWGCNA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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