Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:57 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

BUILD results for SeqGSEA on nebbiolo2


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.

raw results

Package 1768/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.34.0  (landing page)
Xi Wang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/SeqGSEA
git_branch: RELEASE_3_14
git_last_commit: 055cbb6
git_last_commit_date: 2021-10-26 12:07:38 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SeqGSEA
Version: 1.34.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SeqGSEA
StartedAt: 2022-04-12 05:54:20 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 05:57:07 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 166.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SeqGSEA
###
##############################################################################
##############################################################################


* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* preparing ‘SeqGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- 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, 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 c(from, to) :
  closing unused connection 7 (<-localhost:11339)
Warning in c(from, to) :
  closing unused connection 6 (<-localhost:11339)
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Ensembl site unresponsive, trying uswest mirror

Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics:
 chunk 34 (label = main_gsea) 
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate

--- failed re-building ‘SeqGSEA.Rnw’

SUMMARY: processing the following file failed:
  ‘SeqGSEA.Rnw’

Error: Vignette re-building failed.
Execution halted