annotate 1.17.3
Biocore Team c/o BioC user list
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate | | Last Changed Rev: 28881 / Revision: 29143 | | Last Changed Date: 2007-11-21 09:05:51 -0800 (Wed, 21 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | [ WARNINGS ] | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | WARNINGS | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/annotate.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.17.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'annotate' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating annotate-Ex.R ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'p2LL' is deprecated.
Deprecated functions may be defunct as soon as of the next release of R.
See ?Deprecated.
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './annotate.tex' ...
Package natbib Warning: Citation `PubMedRnews' on page 1 undefined on input lin
Package natbib Warning: Citation `PubMedVignette' on page 1 undefined on input
Package natbib Warning: Citation `ChromLocVignette' on page 1 undefined on inpu
Package natbib Warning: Citation `HTMLVignette' on page 1 undefined on input li
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './annotate.tex' ...
Package natbib Warning: Citation `PubMedRnews' on page 1 undefined on input lin
Package natbib Warning: Citation `PubMedVignette' on page 1 undefined on input
Package natbib Warning: Citation `ChromLocVignette' on page 1 undefined on inpu
Package natbib Warning: Citation `HTMLVignette' on page 1 undefined on input li
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './annotate.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './annotate.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './chromLoc.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './chromLoc.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GOusage.tex' ...
Package natbib Warning: Citation `GO' on page 1 undefined on input line 49.
Package natbib Warning: Citation `GOA' on page 1 undefined on input line 52.
Package natbib Warning: Citation `GOA' on page 1 undefined on input line 71.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GOusage.tex' ...
Package natbib Warning: Citation `GO' on page 1 undefined on input line 49.
Package natbib Warning: Citation `GOA' on page 1 undefined on input line 52.
Package natbib Warning: Citation `GOA' on page 1 undefined on input line 71.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GOusage.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './prettyOutput.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './prettyOutput.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './query.tex' ...
Package natbib Warning: Citation `PubMedRnews' on page 1 undefined on input lin
Package natbib Warning: Citation `XML' on page 2 undefined on input line 85.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './query.tex' ...
Package natbib Warning: Citation `PubMedRnews' on page 1 undefined on input lin
Package natbib Warning: Citation `XML' on page 2 undefined on input line 85.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './query.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './useDataPkgs.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './useDataPkgs.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './useHomology.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './useHomology.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './useProbeInfo.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './useProbeInfo.tex' ...
* creating annotate-manual.tex ... OK
* checking annotate-manual.tex ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/annotate.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/annotate.Rcheck
* Installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
** help
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \note
Note: removing empty section \details
Note: removing empty section \references
Note: removing empty section \seealso
>>> Building/Updating help pages for package 'annotate'
Formats: text html latex example
ACCNUMStats text html latex example
GO2heatmap text html latex example
GOmnplot text html latex example
HTMLPage-class text html latex example
LL2homology text html latex example
PMIDAmat text html latex example
PWAmat text html latex example
UniGeneQuery text html latex example
accessionToUID text html latex example
annPkgName text html latex example
aqListGOIDs text html latex example
buildChromLocation text html latex example
buildPubMedAbst text html latex example
chrCats text html latex example
chromLocation-class text html latex example
compatibleVersions text html latex example
dropECode text html latex example
filterGOByOntology text html latex example
findNeighbors text html latex example
genbank text html latex example
genelocator text html latex example
getAnnMap text html latex example
getEvidence text html latex example
getGOTerm text html latex example
getOntology text html latex example
getPMInfo text html latex example
getSYMBOL text html latex example
getSeq4Acc text html latex example
getTDRows text html latex
hasGOannote text html latex example
hgByChroms text html latex example
hgCLengths text html latex example
hgu95AProbLocs text html latex
hgu95Achroloc text html latex example
hgu95Achrom text html latex example
hgu95All text html latex example
hgu95Asym text html latex example
homoData-class text html latex example
htmlpage text html latex example
locuslinkById text html latex example
locuslinkQuery text html latex example
makeAnchor text html latex example
mapOrgs text html latex
neighborGeneFinder text html latex example
p2LL text html latex example
pm.abstGrep text html latex example
pm.getabst text html latex example
pm.titles text html latex example
pmAbst2HTML text html latex example
pmid2MIAME text html latex example
pmidQuery text html latex example
probesByLL text html latex example
pubMedAbst-class text html latex example
pubmed text html latex example
readGEOAnn text html latex example
serializeEnv text html latex example
usedChromGenes text html latex example
** building package indices ...
* DONE (annotate)