PAnnBuilder 1.37.0
Li Hong
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PAnnBuilder | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PAnnBuilder
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* checking for file ‘PAnnBuilder/DESCRIPTION’ ... OK
* preparing ‘PAnnBuilder’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: RSQLite
Loading required package: DBI
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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationDbi
Loading required package: stats4
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
org.Hs.ipiGENEID package:org.Hs.ipi.db R Documentation
_M_a_p _p_r_o_t_e_i_n _i_d_e_n_t_i_f_i_e_r _t_o _E_n_t_r_e_z _g_e_n_e _i_d_e_n_t_i_f_i_e_r
_D_e_s_c_r_i_p_t_i_o_n:
org.Hs.ipiGENEID maps protein identifiers to Entrez Gene
identifiers.
_D_e_t_a_i_l_s:
Mappings were based on data provided by: IPI (<URL:
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.dat.gz>)
on Homo sapiens 3.75, 19 Aug 2010
_E_x_a_m_p_l_e_s:
x <- org.Hs.ipiGENEID
# Get the protein identifiers that are mapped to Entrez gene identifier.
mapped_proteins <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_proteins])
if(length(xx) > 0){
# Get the value of the first key
xx[[1]]
# Get the values for a few keys
if(length(xx) >= 3){
xx[1:3]
}
}
trying URL 'http://gpcr2.biocomp.unibo.it/bacello/dataset.htm'
Content type 'text/html; charset=iso-8859-1' length 5062 bytes
==================================================
downloaded 5062 bytes
sh: wget: command not found
Warning in download.file(srcUrl, fileName, method = "wget", quiet = TRUE) :
download had nonzero exit status
[file87c4bdd901aanimals_dataset.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of file87c4bdd901aanimals_dataset.zip or
file87c4bdd901aanimals_dataset.zip.zip, and cannot find file87c4bdd901aanimals_dataset.zip.ZIP, period.
Warning: running command '/usr/bin/unzip -q file87c4bdd901aanimals_dataset.zip' had status 9
sh: wget: command not found
Warning in download.file(srcUrl, fileName, method = "wget", quiet = TRUE) :
download had nonzero exit status
[file87c3f1fc1dffungi_dataset.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of file87c3f1fc1dffungi_dataset.zip or
file87c3f1fc1dffungi_dataset.zip.zip, and cannot find file87c3f1fc1dffungi_dataset.zip.ZIP, period.
Warning: running command '/usr/bin/unzip -q file87c3f1fc1dffungi_dataset.zip' had status 9
sh: wget: command not found
Warning in download.file(srcUrl, fileName, method = "wget", quiet = TRUE) :
download had nonzero exit status
[file87c3df137d9plants_dataset.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of file87c3df137d9plants_dataset.zip or
file87c3df137d9plants_dataset.zip.zip, and cannot find file87c3df137d9plants_dataset.zip.ZIP, period.
Warning: running command '/usr/bin/unzip -q file87c3df137d9plants_dataset.zip' had status 9
Warning in .local(conn, ...) : Closing open result set
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'PAnnBuilder.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error:
"shell escape" (or "write18") is not enabled:
auto-pst-pdf will not work!
.
! Emergency stop.
...
l.134 Or turn off auto-pst-pdf.}
%
! ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted