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CHECK report for altcdfenvs on merida1

This page was generated on 2019-04-16 11:54:07 -0400 (Tue, 16 Apr 2019).

Package 42/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
altcdfenvs 2.44.0
Laurent Gautier
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/altcdfenvs
Branch: RELEASE_3_8
Last Commit: d804f64
Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: altcdfenvs
Version: 2.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:altcdfenvs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings altcdfenvs_2.44.0.tar.gz
StartedAt: 2019-04-15 22:19:18 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:21:20 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 122.2 seconds
RetCode: 0
Status:  OK 
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:altcdfenvs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings altcdfenvs_2.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/altcdfenvs.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.44.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘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 ... 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
  ‘validObject’
buildCdfEnv.biostrings: no visible global function definition for ‘is’
buildCdfEnv.biostrings: no visible global function definition for ‘new’
buildCdfEnv.biostrings: no visible global function definition for
  ‘update’
buildCdfEnv.biostrings: no visible global function definition for
  ‘xy2indices’
buildCdfEnv.matchprobes: no visible global function definition for ‘is’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘new’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘update’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘xy2indices’
copyCdfEnvAffy: no visible global function definition for ‘copyEnv’
countduplicated: no visible global function definition for ‘is’
countduplicated: no visible global function definition for ‘as’
geneNames.CdfEnvAffy: no visible global function definition for ‘as’
getCdfEnvAffy: no visible global function definition for ‘is’
getCdfEnvAffy: no visible global function definition for ‘getCdfInfo’
index2xy.CdfEnvAffy: no visible global function definition for
  ‘indices2xy’
indexProbes.CdfEnvAffy: no visible global function definition for ‘as’
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’
matchAffyProbes: no visible global function definition for ‘new’
removeIndex: no visible global function definition for ‘as’
unique.CdfEnvAffy: no visible global function definition for ‘as’
validAffyBatch: no visible global function definition for ‘is’
validCdfEnvAffy: no visible global function definition for ‘as’
wrapCdfEnvAffy: no visible global function definition for ‘new’
xy2index.CdfEnvAffy: no visible global function definition for
  ‘xy2indices’
[,CdfEnvAffy-character-missing-missing: no visible global function
  definition for ‘as’
coerce,CdfEnvAffy-Cdf: no visible global function definition for ‘new’
combine,AffyProbesMatch-AffyProbesMatch: no visible global function
  definition for ‘new’
geneNames,CdfEnvAffy: no visible global function definition for ‘as’
indexProbes,CdfEnvAffy-character: no visible global function definition
  for ‘as’
show,CdfEnvAffy: no visible global function definition for ‘as’
toHypergraph,AffyProbesMatch : <anonymous>: no visible global function
  definition for ‘Hyperedge’
toHypergraph,AffyProbesMatch: no visible global function definition for
  ‘new’
toHypergraph,CdfEnvAffy : <anonymous>: no visible global function
  definition for ‘Hyperedge’
toHypergraph,CdfEnvAffy: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  DNAString DNAStringSet Hyperedge PDict as copyEnv getCdfInfo
  indices2xy is matchPDict new update validObject xy2indices
Consider adding
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "update")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
removeIndex      10.350  0.047  10.493
matchAffyProbes   6.298  0.328   6.701
CdfEnvAffy-class  5.202  0.112   5.358
* 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-3.8-bioc/meat/altcdfenvs.Rcheck/00check.log’
for details.



Installation output

altcdfenvs.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL altcdfenvs
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘altcdfenvs’ ...
** R
** data
** inst
** byte-compile and prepare 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)

Tests output


Example timings

altcdfenvs.Rcheck/altcdfenvs-Ex.timings

nameusersystemelapsed
AffyProbesMatch-class0.0020.0010.002
CdfEnvAffy-class5.2020.1125.358
appendCdfEnvAffy0.0070.0010.008
cdfenv000
cdfenvEx0.0030.0020.005
getxy.probeseq0.0010.0010.000
index2xy000
matchAffyProbes6.2980.3286.701
plot.CdfEnvAffy000
removeIndex10.350 0.04710.493
unique.CdfEnvAffy0.0000.0000.001
utils.FASTA0.0070.0010.007
validAffyBatch000