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BioC 3.4: CHECK report for altcdfenvs on moscato1

This page was generated on 2016-09-21 03:41:20 -0700 (Wed, 21 Sep 2016).

Package 38/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
altcdfenvs 2.35.0
Laurent Gautier
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/altcdfenvs
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: altcdfenvs
Version: 2.35.0
Command: rm -rf altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && mkdir altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=altcdfenvs.buildbin-libdir altcdfenvs_2.35.0.tar.gz >altcdfenvs.Rcheck\00install.out 2>&1 && cp altcdfenvs.Rcheck\00install.out altcdfenvs-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=altcdfenvs.buildbin-libdir --install="check:altcdfenvs-install.out" --force-multiarch --no-vignettes --timings altcdfenvs_2.35.0.tar.gz
StartedAt: 2016-09-20 03:46:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:50:04 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 188.2 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=altcdfenvs.buildbin-libdir altcdfenvs_2.35.0.tar.gz >altcdfenvs.Rcheck\00install.out 2>&1 && cp altcdfenvs.Rcheck\00install.out altcdfenvs-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=altcdfenvs.buildbin-libdir --install="check:altcdfenvs-install.out" --force-multiarch --no-vignettes --timings altcdfenvs_2.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/altcdfenvs.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.35.0'
* 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     10.22    0.0   11.20
matchAffyProbes  4.97    0.1   11.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
removeIndex      12.63   0.02   12.64
CdfEnvAffy-class  5.21   0.03    5.24
matchAffyProbes   5.07   0.15    5.22
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/altcdfenvs.Rcheck/00check.log'
for details.


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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'altcdfenvs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'altcdfenvs' as altcdfenvs_2.35.0.zip
* DONE (altcdfenvs)

altcdfenvs.Rcheck/examples_i386/altcdfenvs-Ex.timings:

nameusersystemelapsed
AffyProbesMatch-class000
CdfEnvAffy-class4.090.014.85
appendCdfEnvAffy0.010.000.02
cdfenv000
cdfenvEx0.020.000.01
getxy.probeseq000
index2xy000
matchAffyProbes 4.97 0.1011.88
plot.CdfEnvAffy000
removeIndex10.22 0.0011.20
unique.CdfEnvAffy000
utils.FASTA0.020.000.02
validAffyBatch000

altcdfenvs.Rcheck/examples_x64/altcdfenvs-Ex.timings:

nameusersystemelapsed
AffyProbesMatch-class000
CdfEnvAffy-class5.210.035.24
appendCdfEnvAffy0.020.000.01
cdfenv0.000.020.02
cdfenvEx000
getxy.probeseq000
index2xy000
matchAffyProbes5.070.155.22
plot.CdfEnvAffy000
removeIndex12.63 0.0212.64
unique.CdfEnvAffy000
utils.FASTA000
validAffyBatch0.010.000.01