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BioC 3.1: CHECK report for geneplotter on petty

This page was generated on 2015-10-09 09:32:25 -0700 (Fri, 09 Oct 2015).

Package 380/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneplotter 1.46.0
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/geneplotter
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneplotter
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneplotter_1.46.0.tar.gz
StartedAt: 2015-10-08 23:12:37 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:15:30 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 172.7 seconds
RetCode: 0
Status:  OK 
CheckDir: geneplotter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneplotter_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/geneplotter.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneplotter/DESCRIPTION’ ... OK
* this is package ‘geneplotter’ version ‘1.46.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘geneplotter’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/geneplotter.Rcheck/00check.log’
for details.


geneplotter.Rcheck/00install.out:

* installing *source* package ‘geneplotter’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (geneplotter)

geneplotter.Rcheck/geneplotter-Ex.timings:

nameusersystemelapsed
GetColor0.0030.0000.004
Makesense3.6860.1124.143
alongChrom3.6820.0603.801
amplicon.plot0.0010.0010.001
cColor3.5990.0153.618
cPlot3.4460.0133.467
cScale3.2400.0073.248
eset133a0.2010.0100.212
groupedHeatmap0.9860.0201.007
histStack0.0250.0020.037
imageMap0.1180.0120.151
make.chromOrd0.2510.0290.299
multiecdf0.0820.0070.090
openHtmlPage0.0040.0010.005
plotChr2.8820.0722.959
plotExpressionGraph2.0710.0442.165
plotMA0.0190.0010.021
savepng0.3060.0810.427