Xi Wang
| Snapshot Date: 2026-05-07 13:40 -0400 (Thu, 07 May 2026) |
| git_url: https://git.bioconductor.org/packages/SeqGSEA |
| git_branch: RELEASE_3_23 |
| git_last_commit: 4583d0e |
| git_last_commit_date: 2026-04-28 08:37:35 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-08 11:34 -0400 (Fri, 08 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4992 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4725 |
| 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 2029/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqGSEA 1.52.0 (landing page) Xi Wang
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for SeqGSEA in R Universe. | ||||||||||||||
|
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: 1.52.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SeqGSEA_1.52.0.tar.gz |
| StartedAt: 2026-05-08 04:38:19 -0400 (Fri, 08 May 2026) |
| EndedAt: 2026-05-08 04:45:38 -0400 (Fri, 08 May 2026) |
| EllapsedTime: 438.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SeqGSEA_1.52.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-08 08:38:20 UTC
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.52.0’
* 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 loading without being on the library search path ... 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 ... 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 ... 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’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
topDEGenes 10.029 0.127 10.156
DENBStatPermut4GSEA 9.838 0.139 9.978
DEpermutePval 9.357 0.045 9.402
normFactor 5.952 0.108 6.061
topDSGenes 5.972 0.081 6.053
DSpermute4GSEA 5.585 0.163 5.749
DSresultGeneTable 5.365 0.023 5.389
DSpermutePval 5.325 0.004 5.329
DSresultExonTable 5.294 0.006 5.300
topDSExons 5.253 0.015 5.268
scoreNormalization 5.035 0.032 5.068
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SeqGSEA.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Seqinfo
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from ‘package:Biobase’:
rowMedians
Warning: executing %dopar% sequentially: no parallel backend registered
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in for (i in seq_len(n)) { :
closing unused connection 7 (<-localhost:11710)
Warning in for (i in seq_len(n)) { :
closing unused connection 6 (<-localhost:11710)
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics:
chunk 34 (label = main_gsea)
Error in req_perform(request) : HTTP 500 Internal Server Error.
--- failed re-building ‘SeqGSEA.Rnw’
SUMMARY: processing the following file failed:
‘SeqGSEA.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
SeqGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SeqGSEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘SeqGSEA’ ... ** this is package ‘SeqGSEA’ version ‘1.52.0’ ** 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 | 2.280 | 0.080 | 2.359 | |
| DENBStatPermut4GSEA | 9.838 | 0.139 | 9.978 | |
| DENBTest | 1.726 | 0.018 | 1.743 | |
| DEpermutePval | 9.357 | 0.045 | 9.402 | |
| DSpermute4GSEA | 5.585 | 0.163 | 5.749 | |
| DSpermutePval | 5.325 | 0.004 | 5.329 | |
| DSresultExonTable | 5.294 | 0.006 | 5.300 | |
| DSresultGeneTable | 5.365 | 0.023 | 5.389 | |
| GSEAresultTable | 1.583 | 0.044 | 1.627 | |
| GSEnrichAnalyze | 1.553 | 0.001 | 1.555 | |
| ReadCountSet-class | 0.001 | 0.001 | 0.002 | |
| SeqGeneSet-class | 0.001 | 0.000 | 0.001 | |
| calES | 0.005 | 0.001 | 0.007 | |
| calES.perm | 1.489 | 0.002 | 1.492 | |
| convertEnsembl2Symbol | 0.000 | 0.000 | 0.001 | |
| convertSymbol2Ensembl | 0 | 0 | 0 | |
| counts-methods | 0.011 | 0.001 | 0.011 | |
| estiExonNBstat | 0.480 | 0.041 | 0.520 | |
| estiGeneNBstat | 0.486 | 0.006 | 0.491 | |
| exonID | 0.028 | 0.080 | 0.109 | |
| exonTestability | 0.016 | 0.002 | 0.017 | |
| geneID | 0.036 | 0.081 | 0.118 | |
| geneList | 0.004 | 0.000 | 0.004 | |
| genePermuteScore | 0.005 | 0.000 | 0.006 | |
| geneScore | 0.002 | 0.001 | 0.003 | |
| geneSetDescs | 0.001 | 0.001 | 0.003 | |
| geneSetNames | 0.001 | 0.001 | 0.002 | |
| geneSetSize | 0.002 | 0.000 | 0.002 | |
| geneTestability | 0.017 | 0.001 | 0.018 | |
| genpermuteMat | 4.872 | 0.028 | 4.901 | |
| getGeneCount | 0.014 | 0.000 | 0.015 | |
| label | 0.010 | 0.000 | 0.012 | |
| loadExonCountData | 0.000 | 0.001 | 0.001 | |
| loadGenesets | 0.000 | 0.001 | 0.001 | |
| newGeneSets | 0.000 | 0.002 | 0.003 | |
| newReadCountSet | 0.090 | 0.003 | 0.095 | |
| normFactor | 5.952 | 0.108 | 6.061 | |
| plotES | 1.640 | 0.024 | 1.670 | |
| plotGeneScore | 0.100 | 0.002 | 0.102 | |
| plotSig | 1.600 | 0.004 | 1.606 | |
| plotSigGeneSet | 1.551 | 0.003 | 1.553 | |
| rankCombine | 0.009 | 0.000 | 0.009 | |
| runDESeq | 1.115 | 0.004 | 1.119 | |
| runSeqGSEA | 0.002 | 0.000 | 0.001 | |
| scoreNormalization | 5.035 | 0.032 | 5.068 | |
| size | 0.001 | 0.001 | 0.002 | |
| subsetByGenes | 0.029 | 0.000 | 0.029 | |
| topDEGenes | 10.029 | 0.127 | 10.156 | |
| topDSExons | 5.253 | 0.015 | 5.268 | |
| topDSGenes | 5.972 | 0.081 | 6.053 | |
| topGeneSets | 1.535 | 0.002 | 1.538 | |
| writeScores | 0.003 | 0.003 | 0.007 | |
| writeSigGeneSet | 1.485 | 0.001 | 1.487 | |