gskb 1.5.0
Valerie Bares
| Snapshot Date: 2016-09-17 09:20:18 -0700 (Sat, 17 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/gskb | | Last Changed Rev: 3763 / Revision: 3889 | | Last Changed Date: 2016-05-03 14:48:02 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gskb
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* checking for file ‘gskb/DESCRIPTION’ ... OK
* preparing ‘gskb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Bioconductor version 3.4 (BiocInstaller 1.23.9), ?biocLite for help
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.23.9), R 3.3.1 (2016-06-21).
Installing package(s) ‘PGSEA’
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/PGSEA_1.47.0.tar.gz'
Content type 'application/x-gzip' length 1231085 bytes (1.2 MB)
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downloaded 1.2 MB
* installing *source* package ‘PGSEA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PGSEA)
The downloaded source packages are in
‘/tmp/Rtmpd3ugSZ/downloaded_packages’
Old packages: 'BgeeDB', 'BrowserViz', 'EGSEA', 'MultiAssayExperiment',
'R.utils', 'RnBeads', 'SuppDists', 'aws', 'awsMethods', 'curl', 'flowQB',
'jsonlite', 'mgcv', 'pdInfoBuilder', 'puma', 'recount', 'shinydashboard',
'sourcetools', 'vcd'
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, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, 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 objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
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
Warning in file(file, "rt") :
unable to connect to 'bioinformatics.sdstate.edu' on port 80.
Error: processing vignette 'gskb.Rnw' failed with diagnostics:
chunk 4
Error in file(file, "rt") : cannot open the connection
Execution halted