PGSEA 1.50.0
Karl Dykema
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/PGSEA | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
| veracruz2 | 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-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PGSEA
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* checking for file ‘PGSEA/DESCRIPTION’ ... OK
* preparing ‘PGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: KEGG.db
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Loading required package: annaffy
Loading required package: org.Hs.eg.db
Loading required package: GSEABase
Loading required package: annotate
Loading required package: XML
Loading required package: graph
Attaching package: ‘graph’
The following object is masked from ‘package:XML’:
addNode
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7023/matrix/
OK
Found 1 file(s)
GSE7023_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7023/matrix/GSE7023_series_matrix.txt.gz'
Warning in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7023/matrix/GSE7023_series_matrix.txt.gz': HTTP status was '404 Not Found'
Error: processing vignette 'PGSEA2.Rnw' failed with diagnostics:
chunk 1
Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7023/matrix/GSE7023_series_matrix.txt.gz'
Execution halted