PAnnBuilder 1.20.0
Li Hong
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/PAnnBuilder | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| puck5 | Linux (Ubuntu 12.04) / x86_64 | [ ERROR ] | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for file 'PAnnBuilder/DESCRIPTION' ... OK
* preparing 'PAnnBuilder':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: RSQLite
Loading required package: DBI
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object(s) are masked from 'package:stats':
xtabs
The following object(s) are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
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
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 4516 bytes
opened URL
==================================================
downloaded 4516 bytes
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!
.
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted