Xi Wang
| Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/SeqGSEA |
| git_branch: devel |
| git_last_commit: fd1d162 |
| git_last_commit_date: 2024-04-30 10:31:23 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-20 12:15 -0400 (Thu, 20 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4687 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4402 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1893/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqGSEA 1.45.0 (landing page) Xi Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SeqGSEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqGSEA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SeqGSEA |
| Version: 1.45.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqGSEA_1.45.0.tar.gz |
| StartedAt: 2024-06-19 23:04:32 -0400 (Wed, 19 Jun 2024) |
| EndedAt: 2024-06-19 23:10:35 -0400 (Wed, 19 Jun 2024) |
| EllapsedTime: 362.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqGSEA_1.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.45.0’
* 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 ‘SeqGSEA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘estiExonProbVar’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DENBStat4GSEA: no visible global function definition for ‘colData’
DENBStatPermut4GSEA: no visible global function definition for
‘%dopar%’
DENBStatPermut4GSEA: no visible global function definition for
‘foreach’
DENBStatPermut4GSEA: no visible binding for global variable ‘i’
DENBTest: no visible global function definition for ‘colData’
DENBTest: no visible global function definition for ‘p.adjust’
DEpermutePval: no visible global function definition for ‘p.adjust’
DSpermute4GSEA: no visible global function definition for ‘%dopar%’
DSpermute4GSEA: no visible global function definition for ‘foreach’
DSpermute4GSEA : <anonymous>: no visible binding for global variable
‘i’
DSpermutePval: no visible global function definition for ‘p.adjust’
calES.perm: no visible global function definition for ‘%dopar%’
calES.perm: no visible global function definition for ‘foreach’
calES.perm: no visible binding for global variable ‘i’
calES.perm: no visible global function definition for ‘%do%’
calES.perm: no visible binding for global variable ‘j’
loadExonCountData : <anonymous>: no visible global function definition
for ‘read.table’
nbinomTestForMatrices : <anonymous>: no visible global function
definition for ‘dnbinom’
plotES : <anonymous>: no visible global function definition for
‘density’
plotES: no visible global function definition for ‘density’
plotES : <anonymous>: no visible global function definition for
‘points’
plotES: no visible global function definition for ‘points’
plotES: no visible global function definition for ‘colors’
plotES: no visible global function definition for ‘lines’
plotES: no visible global function definition for ‘legend’
plotES: no visible global function definition for ‘dev.off’
plotGeneScore: no visible global function definition for ‘lines’
plotGeneScore: no visible global function definition for ‘colors’
plotGeneScore: no visible global function definition for ‘points’
plotGeneScore: no visible global function definition for ‘matlines’
plotGeneScore: no visible global function definition for ‘legend’
plotGeneScore: no visible global function definition for ‘dev.off’
plotSig: no visible global function definition for ‘points’
plotSig: no visible global function definition for ‘colors’
plotSig: no visible global function definition for ‘legend’
plotSig: no visible global function definition for ‘dev.off’
plotSigGeneSet: no visible global function definition for ‘par’
plotSigGeneSet: no visible global function definition for ‘layout’
plotSigGeneSet: no visible global function definition for ‘lines’
plotSigGeneSet : <anonymous>: no visible global function definition for
‘lines’
plotSigGeneSet: no visible global function definition for ‘colors’
plotSigGeneSet: no visible global function definition for ‘text’
plotSigGeneSet: no visible global function definition for ‘density’
plotSigGeneSet: no visible global function definition for ‘legend’
plotSigGeneSet: no visible global function definition for ‘dev.off’
runDESeq: no visible global function definition for ‘DataFrame’
runSeqGSEA: no visible global function definition for ‘makeCluster’
runSeqGSEA: no visible global function definition for ‘write.table’
signifES : <anonymous>: no visible global function definition for
‘median’
writeScores: no visible global function definition for ‘write.table’
writeSigGeneSet: no visible global function definition for
‘write.table’
Undefined global functions or variables:
%do% %dopar% DataFrame colData colors density dev.off dnbinom foreach
i j layout legend lines makeCluster matlines median p.adjust par
points read.table text write.table
Consider adding
importFrom("grDevices", "colors", "dev.off")
importFrom("graphics", "layout", "legend", "lines", "matlines", "par",
"points", "text")
importFrom("stats", "density", "dnbinom", "median", "p.adjust")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
topDEGenes 11.920 0.079 12.058
DENBStatPermut4GSEA 11.674 0.153 11.995
DEpermutePval 11.597 0.094 11.761
topDSGenes 6.483 0.141 6.669
DSpermute4GSEA 6.224 0.175 6.454
genpermuteMat 5.876 0.170 6.092
scoreNormalization 5.828 0.158 6.060
topDSExons 5.767 0.116 5.949
DSresultExonTable 5.615 0.122 5.775
DSresultGeneTable 5.611 0.104 5.747
DSpermutePval 5.527 0.117 5.676
normFactor 5.540 0.088 5.662
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
SeqGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqGSEA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SeqGSEA’ ... ** using staged installation ** R ** data ** 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 (SeqGSEA)
SeqGSEA.Rcheck/SeqGSEA-Ex.timings
| name | user | system | elapsed | |
| DENBStat4GSEA | 2.557 | 0.127 | 2.721 | |
| DENBStatPermut4GSEA | 11.674 | 0.153 | 11.995 | |
| DENBTest | 2.129 | 0.051 | 2.200 | |
| DEpermutePval | 11.597 | 0.094 | 11.761 | |
| DSpermute4GSEA | 6.224 | 0.175 | 6.454 | |
| DSpermutePval | 5.527 | 0.117 | 5.676 | |
| DSresultExonTable | 5.615 | 0.122 | 5.775 | |
| DSresultGeneTable | 5.611 | 0.104 | 5.747 | |
| GSEAresultTable | 1.801 | 0.035 | 1.865 | |
| GSEnrichAnalyze | 1.828 | 0.015 | 1.854 | |
| ReadCountSet-class | 0.001 | 0.000 | 0.001 | |
| SeqGeneSet-class | 0.001 | 0.000 | 0.001 | |
| calES | 0.007 | 0.003 | 0.011 | |
| calES.perm | 1.766 | 0.011 | 1.786 | |
| convertEnsembl2Symbol | 0 | 0 | 0 | |
| convertSymbol2Ensembl | 0 | 0 | 0 | |
| counts-methods | 0.011 | 0.001 | 0.012 | |
| estiExonNBstat | 0.529 | 0.010 | 0.543 | |
| estiGeneNBstat | 0.549 | 0.017 | 0.569 | |
| exonID | 0.049 | 0.068 | 0.117 | |
| exonTestability | 0.018 | 0.002 | 0.020 | |
| geneID | 0.059 | 0.069 | 0.127 | |
| geneList | 0.004 | 0.000 | 0.004 | |
| genePermuteScore | 0.006 | 0.002 | 0.008 | |
| geneScore | 0.003 | 0.002 | 0.006 | |
| geneSetDescs | 0.002 | 0.001 | 0.003 | |
| geneSetNames | 0.002 | 0.001 | 0.003 | |
| geneSetSize | 0.002 | 0.001 | 0.003 | |
| geneTestability | 0.019 | 0.001 | 0.020 | |
| genpermuteMat | 5.876 | 0.170 | 6.092 | |
| getGeneCount | 0.017 | 0.002 | 0.019 | |
| label | 0.012 | 0.002 | 0.014 | |
| loadExonCountData | 0.001 | 0.001 | 0.002 | |
| loadGenesets | 0 | 0 | 0 | |
| newGeneSets | 0.002 | 0.000 | 0.004 | |
| newReadCountSet | 0.113 | 0.001 | 0.115 | |
| normFactor | 5.540 | 0.088 | 5.662 | |
| plotES | 1.835 | 0.020 | 1.863 | |
| plotGeneScore | 0.111 | 0.006 | 0.121 | |
| plotSig | 1.786 | 0.014 | 1.813 | |
| plotSigGeneSet | 1.760 | 0.015 | 1.784 | |
| rankCombine | 0.006 | 0.003 | 0.009 | |
| runDESeq | 1.311 | 0.009 | 1.327 | |
| runSeqGSEA | 0.001 | 0.001 | 0.003 | |
| scoreNormalization | 5.828 | 0.158 | 6.060 | |
| size | 0.002 | 0.000 | 0.003 | |
| subsetByGenes | 0.031 | 0.002 | 0.033 | |
| topDEGenes | 11.920 | 0.079 | 12.058 | |
| topDSExons | 5.767 | 0.116 | 5.949 | |
| topDSGenes | 6.483 | 0.141 | 6.669 | |
| topGeneSets | 1.882 | 0.021 | 1.922 | |
| writeScores | 0.008 | 0.002 | 0.009 | |
| writeSigGeneSet | 1.799 | 0.017 | 1.831 | |