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BioC 3.2: CHECK report for altcdfenvs on oaxaca

This page was generated on 2016-04-23 10:22:50 -0700 (Sat, 23 Apr 2016).

Package 38/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
altcdfenvs 2.32.0
Laurent Gautier
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/altcdfenvs
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: altcdfenvs
Version: 2.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings altcdfenvs_2.32.0.tar.gz
StartedAt: 2016-04-22 21:45:22 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 21:47:29 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 126.9 seconds
RetCode: 0
Status:  OK 
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings altcdfenvs_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/altcdfenvs.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.32.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘affy’ ‘makecdfenv’ ‘Biostrings’
  ‘hypergraph’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [10s/10s] 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
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildCdfEnv.biostrings: no visible global function definition for
  ‘xy2indices’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘xy2indices’
copyCdfEnvAffy: no visible global function definition for ‘copyEnv’
getCdfEnvAffy: no visible global function definition for ‘getCdfInfo’
index2xy.CdfEnvAffy: no visible global function definition for
  ‘indices2xy’
matchAffyProbes : <anonymous>: no visible global function definition
  for ‘elementLengths’
matchAffyProbes: no visible global function definition for
  ‘DNAStringSet’
matchAffyProbes: no visible global function definition for ‘DNAString’
matchAffyProbes: no visible global function definition for ‘PDict’
matchAffyProbes: no visible global function definition for ‘matchPDict’
xy2index.CdfEnvAffy: no visible global function definition for
  ‘xy2indices’
toHypergraph,AffyProbesMatch : .local : <anonymous>: no visible global
  function definition for ‘Hyperedge’
toHypergraph,CdfEnvAffy : <anonymous>: no visible global function
  definition for ‘Hyperedge’
* 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 ... [26s/27s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
removeIndex     11.021  0.061  11.180
matchAffyProbes  5.661  0.243   6.014
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-class0.0020.0000.002
CdfEnvAffy-class4.4660.0424.844
appendCdfEnvAffy0.0040.0010.006
cdfenv000
cdfenvEx0.0030.0020.004
getxy.probeseq0.0010.0000.001
index2xy0.0010.0010.001
matchAffyProbes5.6610.2436.014
plot.CdfEnvAffy0.0010.0000.000
removeIndex11.021 0.06111.180
unique.CdfEnvAffy000
utils.FASTA0.0060.0000.006
validAffyBatch0.0010.0000.000