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BUILD report for RGSEA on malbec2

This page was generated on 2019-10-16 12:04:45 -0400 (Wed, 16 Oct 2019).

Package 1369/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGSEA 1.18.0
Chengcheng Ma
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RGSEA
Branch: RELEASE_3_9
Last Commit: 6e3b519
Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RGSEA
Version: 1.18.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGSEA
StartedAt: 2019-10-15 20:57:19 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:57:32 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 13.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RGSEA
###
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* checking for file ‘RGSEA/DESCRIPTION’ ... OK
* preparing ‘RGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RGSEA.Rnw’ using knitr
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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,
    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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
File stored at: 
/tmp/RtmpaCPyTL/GDS4100.soft.gz
Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_character(),
  IDENTIFIER = col_character()
)
See spec(...) for full column specifications.
File stored at: 
/tmp/RtmpaCPyTL/GPL570.annot.gz
Warning: 62 parsing failures.
  row             col           expected    actual         file
54614 Platform_SPOTID 1/0/T/F/TRUE/FALSE --Control literal data
54615 Platform_SPOTID 1/0/T/F/TRUE/FALSE --Control literal data
54616 Platform_SPOTID 1/0/T/F/TRUE/FALSE --Control literal data
54617 Platform_SPOTID 1/0/T/F/TRUE/FALSE --Control literal data
54618 Platform_SPOTID 1/0/T/F/TRUE/FALSE --Control literal data
..... ............... .................. ......... ............
See problems(...) for more details.

Warning in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4102/soft/GDS4102.soft.gz': HTTP status was '404 Not Found'
Quitting from lines 84-87 (RGSEA.Rnw) 
Error: processing vignette 'RGSEA.Rnw' failed with diagnostics:
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4102/soft/GDS4102.soft.gz'
--- failed re-building ‘RGSEA.Rnw’

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

Error: Vignette re-building failed.
Execution halted