Xi Wang
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/SeqGSEA |
| git_branch: devel |
| git_last_commit: eb9808f |
| git_last_commit_date: 2024-10-29 09:45:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:39 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1924/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqGSEA 1.47.0 (landing page) Xi Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SeqGSEA |
| Version: 1.47.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SeqGSEA_1.47.0.tar.gz |
| StartedAt: 2025-01-25 11:36:07 -0000 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 11:43:08 -0000 (Sat, 25 Jan 2025) |
| EllapsedTime: 421.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: 6 |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SeqGSEA_1.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.47.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/SeqGSEA.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
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 whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ReadCountSet-class.Rd: eSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
Warning: program compiled against libxml 212 using older 211
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
topDEGenes 13.205 0.048 13.282
DENBStatPermut4GSEA 12.831 0.164 13.024
DEpermutePval 12.756 0.036 12.821
DSpermute4GSEA 8.806 0.088 8.914
DSresultExonTable 8.677 0.048 8.744
topDSGenes 8.696 0.008 8.726
DSresultGeneTable 8.697 0.004 8.722
genpermuteMat 8.588 0.096 8.704
normFactor 8.492 0.028 8.540
DSpermutePval 8.468 0.036 8.523
topDSExons 8.442 0.027 8.492
scoreNormalization 8.352 0.028 8.399
* 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: 6 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
SeqGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SeqGSEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘SeqGSEA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (SeqGSEA)
SeqGSEA.Rcheck/SeqGSEA-Ex.timings
| name | user | system | elapsed | |
| DENBStat4GSEA | 1.965 | 0.164 | 2.133 | |
| DENBStatPermut4GSEA | 12.831 | 0.164 | 13.024 | |
| DENBTest | 2.529 | 0.020 | 2.553 | |
| DEpermutePval | 12.756 | 0.036 | 12.821 | |
| DSpermute4GSEA | 8.806 | 0.088 | 8.914 | |
| DSpermutePval | 8.468 | 0.036 | 8.523 | |
| DSresultExonTable | 8.677 | 0.048 | 8.744 | |
| DSresultGeneTable | 8.697 | 0.004 | 8.722 | |
| GSEAresultTable | 2.288 | 0.036 | 2.330 | |
| GSEnrichAnalyze | 2.218 | 0.035 | 2.259 | |
| ReadCountSet-class | 0.002 | 0.000 | 0.001 | |
| SeqGeneSet-class | 0.001 | 0.000 | 0.000 | |
| calES | 0.007 | 0.000 | 0.006 | |
| calES.perm | 2.274 | 0.000 | 2.281 | |
| convertEnsembl2Symbol | 0.001 | 0.000 | 0.000 | |
| convertSymbol2Ensembl | 0 | 0 | 0 | |
| counts-methods | 0.007 | 0.004 | 0.012 | |
| estiExonNBstat | 0.792 | 0.016 | 0.810 | |
| estiGeneNBstat | 0.804 | 0.004 | 0.809 | |
| exonID | 0.023 | 0.016 | 0.039 | |
| exonTestability | 0.017 | 0.003 | 0.020 | |
| geneID | 0.042 | 0.004 | 0.046 | |
| geneList | 0.005 | 0.000 | 0.005 | |
| genePermuteScore | 0.006 | 0.000 | 0.006 | |
| geneScore | 0.003 | 0.000 | 0.003 | |
| geneSetDescs | 0.002 | 0.000 | 0.002 | |
| geneSetNames | 0.002 | 0.000 | 0.002 | |
| geneSetSize | 0.002 | 0.000 | 0.002 | |
| geneTestability | 0.021 | 0.000 | 0.022 | |
| genpermuteMat | 8.588 | 0.096 | 8.704 | |
| getGeneCount | 0.018 | 0.000 | 0.019 | |
| label | 0.011 | 0.000 | 0.011 | |
| loadExonCountData | 0.001 | 0.000 | 0.001 | |
| loadGenesets | 0 | 0 | 0 | |
| newGeneSets | 0.002 | 0.000 | 0.003 | |
| newReadCountSet | 0.117 | 0.000 | 0.117 | |
| normFactor | 8.492 | 0.028 | 8.540 | |
| plotES | 2.339 | 0.076 | 2.420 | |
| plotGeneScore | 0.124 | 0.004 | 0.128 | |
| plotSig | 2.238 | 0.000 | 2.243 | |
| plotSigGeneSet | 2.258 | 0.000 | 2.264 | |
| rankCombine | 0.005 | 0.004 | 0.009 | |
| runDESeq | 1.516 | 0.000 | 1.520 | |
| runSeqGSEA | 0.002 | 0.000 | 0.002 | |
| scoreNormalization | 8.352 | 0.028 | 8.399 | |
| size | 0.002 | 0.000 | 0.002 | |
| subsetByGenes | 0.035 | 0.000 | 0.035 | |
| topDEGenes | 13.205 | 0.048 | 13.282 | |
| topDSExons | 8.442 | 0.027 | 8.492 | |
| topDSGenes | 8.696 | 0.008 | 8.726 | |
| topGeneSets | 2.289 | 0.060 | 2.353 | |
| writeScores | 0.007 | 0.000 | 0.007 | |
| writeSigGeneSet | 2.297 | 0.012 | 2.319 | |