| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-27 02:34:43 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 | ||||
|
To the developers/maintainers of the SeqGSEA package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1836/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqGSEA 1.39.0 (landing page) Xi Wang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: SeqGSEA |
| Version: 1.39.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SeqGSEA_1.39.0.tar.gz |
| StartedAt: 2023-02-24 18:23:43 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 18:35:25 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 702.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SeqGSEA_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.39.0’
* 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 R 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DENBStatPermut4GSEA 15.615 0.252 15.868
topDEGenes 15.512 0.112 15.656
DEpermutePval 14.979 0.196 15.175
topDSGenes 9.574 0.096 9.670
normFactor 9.461 0.132 9.593
DSpermute4GSEA 8.823 0.152 8.976
topDSExons 8.910 0.040 8.950
DSresultGeneTable 8.808 0.048 8.857
DSresultExonTable 8.749 0.052 8.800
scoreNormalization 8.707 0.036 8.744
DSpermutePval 8.642 0.068 8.711
genpermuteMat 8.053 0.032 8.085
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SeqGSEA.Rnw’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘SeqGSEA.Rnw’
...
> gene.score.perm <- genePermuteScore(DEscore.perm,
+ DSscore.perm, DEweight = 0.5)
> gene.set <- loadGenesets(geneset.file, geneIDs, geneID.type = "ensembl",
+ genesetsize.min = 5, genesetsize.max = 1000)
When sourcing ‘SeqGSEA.R’:
Error: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 350312 bytes received
Execution halted
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘SeqGSEA.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, 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 objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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:11362)
Warning in for (i in seq_len(n)) { :
closing unused connection 6 (<-localhost:11362)
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics:
chunk 38 (label = main_gsea_DE)
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 462953 bytes received
--- 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-3.17-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
SeqGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SeqGSEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 2.445 | 0.120 | 2.565 | |
| DENBStatPermut4GSEA | 15.615 | 0.252 | 15.868 | |
| DENBTest | 2.713 | 0.035 | 2.748 | |
| DEpermutePval | 14.979 | 0.196 | 15.175 | |
| DSpermute4GSEA | 8.823 | 0.152 | 8.976 | |
| DSpermutePval | 8.642 | 0.068 | 8.711 | |
| DSresultExonTable | 8.749 | 0.052 | 8.800 | |
| DSresultGeneTable | 8.808 | 0.048 | 8.857 | |
| GSEAresultTable | 2.264 | 0.028 | 2.292 | |
| GSEnrichAnalyze | 2.172 | 0.003 | 2.175 | |
| ReadCountSet-class | 0.002 | 0.000 | 0.001 | |
| SeqGeneSet-class | 0.000 | 0.001 | 0.001 | |
| calES | 0.005 | 0.002 | 0.006 | |
| calES.perm | 2.213 | 0.004 | 2.217 | |
| convertEnsembl2Symbol | 0.000 | 0.000 | 0.001 | |
| convertSymbol2Ensembl | 0 | 0 | 0 | |
| counts-methods | 0.015 | 0.000 | 0.015 | |
| estiExonNBstat | 0.787 | 0.020 | 0.807 | |
| estiGeneNBstat | 0.81 | 0.00 | 0.81 | |
| exonID | 0.017 | 0.048 | 0.065 | |
| exonTestability | 0.038 | 0.004 | 0.042 | |
| geneID | 0.043 | 0.028 | 0.071 | |
| geneList | 0.005 | 0.000 | 0.005 | |
| genePermuteScore | 0.007 | 0.000 | 0.007 | |
| geneScore | 0.003 | 0.000 | 0.003 | |
| geneSetDescs | 0.002 | 0.000 | 0.002 | |
| geneSetNames | 0.002 | 0.000 | 0.002 | |
| geneSetSize | 0.002 | 0.001 | 0.002 | |
| geneTestability | 0.022 | 0.003 | 0.025 | |
| genpermuteMat | 8.053 | 0.032 | 8.085 | |
| getGeneCount | 0.024 | 0.000 | 0.024 | |
| label | 0.015 | 0.000 | 0.015 | |
| loadExonCountData | 0.000 | 0.001 | 0.001 | |
| loadGenesets | 0 | 0 | 0 | |
| newGeneSets | 0.002 | 0.000 | 0.003 | |
| newReadCountSet | 0.128 | 0.004 | 0.132 | |
| normFactor | 9.461 | 0.132 | 9.593 | |
| plotES | 2.329 | 0.008 | 2.337 | |
| plotGeneScore | 0.124 | 0.000 | 0.125 | |
| plotSig | 2.219 | 0.000 | 2.219 | |
| plotSigGeneSet | 2.248 | 0.023 | 2.271 | |
| rankCombine | 0.01 | 0.00 | 0.01 | |
| runDESeq | 1.788 | 0.004 | 1.791 | |
| runSeqGSEA | 0.002 | 0.000 | 0.002 | |
| scoreNormalization | 8.707 | 0.036 | 8.744 | |
| size | 0.002 | 0.000 | 0.003 | |
| subsetByGenes | 0.037 | 0.000 | 0.037 | |
| topDEGenes | 15.512 | 0.112 | 15.656 | |
| topDSExons | 8.91 | 0.04 | 8.95 | |
| topDSGenes | 9.574 | 0.096 | 9.670 | |
| topGeneSets | 2.230 | 0.004 | 2.235 | |
| writeScores | 0.003 | 0.004 | 0.007 | |
| writeSigGeneSet | 2.249 | 0.004 | 2.253 | |