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BioC 2.13: CHECK report for altcdfenvs on perceval

This page was generated on 2014-04-05 09:51:40 -0700 (Sat, 05 Apr 2014).

Package 33/750HostnameOS / ArchBUILDCHECKBUILD BIN
altcdfenvs 2.24.0
Laurent Gautier
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/altcdfenvs
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: altcdfenvs
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch altcdfenvs_2.24.0.tar.gz
StartedAt: 2014-04-04 23:19:48 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:24:01 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 252.6 seconds
RetCode: 0
Status:  OK 
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/altcdfenvs.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.24.0’
* 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 ‘altcdfenvs’ can be installed ... [16s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘Biostrings’ ‘hypergraph’ ‘makecdfenv’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘altcdfenvs.Rnw’, ‘modify.Rnw’, ‘ngenomeschips.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
matchAffyProbes  21.711  0.995  23.126
removeIndex      21.866  0.300  22.932
CdfEnvAffy-class  8.507  0.168   9.152
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/altcdfenvs.Rcheck/00check.log’
for details.

altcdfenvs.Rcheck/00install.out:

* installing *source* package ‘altcdfenvs’ ...
** R
** data
** inst
** preparing package for lazy loading
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for ‘toHypergraph’ with signature ‘"CdfEnvAffy"’: no definition for class “CdfEnvAffy”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (altcdfenvs)

altcdfenvs.Rcheck/altcdfenvs-Ex.timings:

nameusersystemelapsed
AffyProbesMatch-class0.0090.0010.011
CdfEnvAffy-class8.5070.1689.152
appendCdfEnvAffy0.050.010.06
cdfenv0.0080.0020.010
cdfenvEx0.0180.0030.021
getxy.probeseq0.0080.0010.009
index2xy0.0090.0010.010
matchAffyProbes21.711 0.99523.126
plot.CdfEnvAffy0.0010.0040.005
removeIndex21.866 0.30022.932
unique.CdfEnvAffy0.0020.0040.006
utils.FASTA0.0120.0110.023
validAffyBatch0.0010.0040.007