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CHECK report for altcdfenvs on tokay1

This page was generated on 2018-04-12 13:17:29 -0400 (Thu, 12 Apr 2018).

Package 38/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
altcdfenvs 2.40.0
Laurent Gautier
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/altcdfenvs
Branch: RELEASE_3_6
Last Commit: 517a208
Last Changed Date: 2017-10-30 12:39:01 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: altcdfenvs
Version: 2.40.0
Command: rm -rf altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && mkdir altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=altcdfenvs.buildbin-libdir altcdfenvs_2.40.0.tar.gz >altcdfenvs.Rcheck\00install.out 2>&1 && cp altcdfenvs.Rcheck\00install.out altcdfenvs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=altcdfenvs.buildbin-libdir --install="check:altcdfenvs-install.out" --force-multiarch --no-vignettes --timings altcdfenvs_2.40.0.tar.gz
StartedAt: 2018-04-11 22:10:08 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:12:53 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 165.2 seconds
RetCode: 0
Status:  OK  
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && mkdir altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=altcdfenvs.buildbin-libdir altcdfenvs_2.40.0.tar.gz >altcdfenvs.Rcheck\00install.out 2>&1 && cp altcdfenvs.Rcheck\00install.out altcdfenvs-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=altcdfenvs.buildbin-libdir --install="check:altcdfenvs-install.out" --force-multiarch --no-vignettes --timings altcdfenvs_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/altcdfenvs.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.40.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
removeIndex      7.42   0.02    8.39
matchAffyProbes  6.13   0.22    7.76
CdfEnvAffy-class 4.09   0.02    6.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
removeIndex     8.63   0.04    8.67
matchAffyProbes 6.59   0.14    6.74
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/altcdfenvs.Rcheck/00check.log'
for details.



Installation output

altcdfenvs.Rcheck/00install.out


install for i386

* 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
  converting help for package 'altcdfenvs'
    finding HTML links ... done
    AffyProbesMatch-class                   html  
    CdfEnvAffy-class                        html  
    appendCdfEnvAffy                        html  
    buildCdfEnv.biostrings                  html  
    cdfenv                                  html  
    cdfenvEx                                html  
    copyCdfEnvAffy                          html  
    countduplicated                         html  
    geneNames                               html  
    getxy.probeseq                          html  
    index2xy                                html  
    indexProbes.CdfEnvAffy                  html  
    matchAffyProbes                         html  
    plot.CdfEnvAffy                         html  
    removeIndex                             html  
    toHypergraph                            html  
    unique.CdfEnvAffy                       html  
    utils.FASTA                             html  
    validAffyBatch                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'altcdfenvs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'altcdfenvs' as altcdfenvs_2.40.0.zip
* DONE (altcdfenvs)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

altcdfenvs.Rcheck/examples_i386/altcdfenvs-Ex.timings

nameusersystemelapsed
AffyProbesMatch-class000
CdfEnvAffy-class4.090.026.78
appendCdfEnvAffy0.010.010.04
cdfenv000
cdfenvEx000
getxy.probeseq0.010.000.02
index2xy000
matchAffyProbes6.130.227.76
plot.CdfEnvAffy000
removeIndex7.420.028.39
unique.CdfEnvAffy000
utils.FASTA0.040.000.03
validAffyBatch000

altcdfenvs.Rcheck/examples_x64/altcdfenvs-Ex.timings

nameusersystemelapsed
AffyProbesMatch-class000
CdfEnvAffy-class3.690.053.74
appendCdfEnvAffy0.010.020.04
cdfenv000
cdfenvEx000
getxy.probeseq000
index2xy000
matchAffyProbes6.590.146.74
plot.CdfEnvAffy000
removeIndex8.630.048.67
unique.CdfEnvAffy000
utils.FASTA0.030.000.03
validAffyBatch000