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 |  |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /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