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BioC 3.4: CHECK report for GOstats on tokay1

This page was generated on 2017-04-15 16:14:31 -0400 (Sat, 15 Apr 2017).

Package 547/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOstats 2.40.0
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GOstats
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOstats
Version: 2.40.0
Command: rm -rf GOstats.buildbin-libdir GOstats.Rcheck && mkdir GOstats.buildbin-libdir GOstats.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOstats.buildbin-libdir GOstats_2.40.0.tar.gz >GOstats.Rcheck\00install.out 2>&1 && cp GOstats.Rcheck\00install.out GOstats-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GOstats.buildbin-libdir --install="check:GOstats-install.out" --force-multiarch --no-vignettes --timings GOstats_2.40.0.tar.gz
StartedAt: 2017-04-14 22:46:32 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:51:17 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 284.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GOstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOstats.buildbin-libdir GOstats.Rcheck && mkdir GOstats.buildbin-libdir GOstats.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOstats.buildbin-libdir GOstats_2.40.0.tar.gz >GOstats.Rcheck\00install.out 2>&1 && cp GOstats.Rcheck\00install.out GOstats-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GOstats.buildbin-libdir --install="check:GOstats-install.out" --force-multiarch --no-vignettes --timings GOstats_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/GOstats.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.40.0'
* 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 whether package 'GOstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'Category' 'graph' 'GO.db' 'annotate'
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls in package code:
  'Rgraphviz' 'SparseM'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'Category:::XXX_getSummaryGeneric_XXX'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compCorrGraph: no visible global function definition for
  'as.matrix.csr'
plotGOTermGraph: no visible global function definition for
  'makeNodeAttrs'
Undefined global functions or variables:
  as.matrix.csr makeNodeAttrs
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/GOstats.Rcheck/00check.log'
for details.


GOstats.Rcheck/00install.out:


install for i386

* installing *source* package 'GOstats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GOstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOstats' as GOstats_2.40.0.zip
* DONE (GOstats)

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

nameusersystemelapsed
Ndists0.050.020.07
compCorrGraph0.410.000.40
compGdist0.070.010.10
idx2dimnames0.050.000.04
makeGOGraph1.220.051.27
notConn0.020.010.03
oneGOGraph0.480.020.53
probeSetSummary1.940.062.00
shortestPath2.810.032.84
simLL0.700.000.71
triadCensus000

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

nameusersystemelapsed
Ndists0.070.000.06
compCorrGraph0.150.000.15
compGdist0.10.00.1
idx2dimnames0.010.020.03
makeGOGraph1.070.031.09
notConn0.010.010.03
oneGOGraph0.420.020.44
probeSetSummary2.280.052.33
shortestPath4.370.034.40
simLL0.820.000.81
triadCensus000