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Package 212/553HostnameOS / ArchBUILDCHECKBUILD BIN
geneplotter 1.34.0
Bioconductor Package Maintainer
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/geneplotter
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
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 

Summary

Package: geneplotter
Version: 1.34.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings geneplotter_1.34.0.tar.gz
StartedAt: 2012-09-24 01:01:58 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:04:26 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 148.4 seconds
RetCode: 0
Status:  OK 
CheckDir: geneplotter.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/geneplotter.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneplotter/DESCRIPTION’ ... OK
* this is package ‘geneplotter’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘geneplotter’ can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
amplicon.plot: warning in mget(featureNames(ESET), env = get(dname),
  ifnotfound = NA): partial argument match of 'env' to 'envir'
cColor: warning in mget(probes, env = probesToChrom(plotChroms),
  ifnotfound = NA): partial argument match of 'env' to 'envir'
getACGeneSyms: warning in mget(affys, env = geneSymbols(chrObj),
  ifnotfound = NA): partial argument match of 'env' to 'envir'
make.chromOrd: warning in mget(gnames, env = get(clname), ifnotfound =
  NA): partial argument match of 'env' to 'envir'
make.chromOrd: warning in mget(gnames, env = get(dname), ifnotfound =
  NA): partial argument match of 'env' to 'envir'
plotChr: warning in mget(labs, env = get(paste(senseObj$lib, "SYMBOL",
  sep = "")), ifnotfound = NA): partial argument match of 'env' to
  'envir'
plotChr: warning in mget(lines.at, env = get(paste(senseObj$lib,
  "CHRLOC", sep = "")), ifnotfound = NA): partial argument match of
  'env' to 'envir'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/geneplotter.Rcheck/00check.log’
for details.

geneplotter.Rcheck/00install.out:

* installing *source* package ‘geneplotter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘byChroms.Rnw’ 
   ‘visualize.Rnw’ 
** testing if installed package can be loaded

* DONE (geneplotter)

geneplotter.Rcheck/geneplotter-Ex.timings:

nameusersystemelapsed
GetColor0.0000.0000.003
Makesense4.4320.0804.928
alongChrom2.1200.0402.171
amplicon.plot000
cColor1.8560.0241.885
cPlot1.5120.0041.523
cScale1.4690.0081.476
eset133a0.1080.0160.124
groupedHeatmap0.6360.0000.640
histStack0.0160.0040.021
imageMap0.0960.0000.161
make.chromOrd0.1680.0080.218
multiecdf0.0840.0000.085
openHtmlPage0.0000.0000.002
plotChr3.3120.0283.417
plotExpressionGraph1.5520.0241.666
savepng0.1600.0680.280