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BioC 3.1: CHECK report for Biobase on moscato2

This page was generated on 2015-10-09 09:27:01 -0700 (Fri, 09 Oct 2015).

Package 89/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.28.0
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/Biobase
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: Biobase
Version: 2.28.0
Command: rm -rf Biobase.buildbin-libdir Biobase.Rcheck && mkdir Biobase.buildbin-libdir Biobase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Biobase.buildbin-libdir Biobase_2.28.0.tar.gz >Biobase.Rcheck\00install.out 2>&1 && cp Biobase.Rcheck\00install.out Biobase-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Biobase.buildbin-libdir --install="check:Biobase-install.out" --force-multiarch --no-vignettes --timings Biobase_2.28.0.tar.gz
StartedAt: 2015-10-08 23:38:10 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:41:24 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 194.4 seconds
RetCode: 0
Status:  OK  
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Biobase.buildbin-libdir Biobase.Rcheck && mkdir Biobase.buildbin-libdir Biobase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Biobase.buildbin-libdir Biobase_2.28.0.tar.gz >Biobase.Rcheck\00install.out 2>&1 && cp Biobase.Rcheck\00install.out Biobase-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Biobase.buildbin-libdir --install="check:Biobase-install.out" --force-multiarch --no-vignettes --timings Biobase_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/Biobase.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.28.0'
* 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 'Biobase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.1-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/i386/Biobase.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/x64/Biobase.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [6s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [20s]
  Running 'test-rowMedians.R' [24s]
 [44s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [26s]
  Running 'test-rowMedians.R' [29s]
 [55s] 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: 1 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/Biobase.Rcheck/00check.log'
for details.


Biobase.Rcheck/00install.out:


install for i386

* installing *source* package 'Biobase' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c envir.c -o envir.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matchpt.c -o matchpt.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rowMedians.c -o rowMedians.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sublist_extract.c -o sublist_extract.o
gcc -m32 -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/i386
** 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 'Biobase' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c envir.c -o envir.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matchpt.c -o matchpt.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rowMedians.c -o rowMedians.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sublist_extract.c -o sublist_extract.o
gcc -m64 -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biobase' as Biobase_2.28.0.zip
* DONE (Biobase)

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

nameusersystemelapsed
Aggregate000
ScalarObject-class0.030.000.03
addVig2Menu000
anyMissing000
cache0.010.000.14
channel0.170.000.17
channelNames0.080.000.08
class.AnnotatedDataFrame0.060.000.06
class.ExpressionSet0.360.000.36
class.MIAxE0.030.000.03
class.MultiSet0.050.000.05
class.NChannelSet0.380.000.37
class.Versioned0.090.000.10
class.VersionedBiobase0.050.000.04
class.Versions0.030.000.03
class.VersionsNull000
class.container0.010.000.02
class.eSet0.140.000.14
classVersion000
contents000
copyEnv0.010.000.02
copySubstitute0.000.000.02
createPackage000
data.aaMap0.000.020.02
data.geneData0.060.000.06
data.reporter0.020.000.02
data.sample.ExpressionSet0.030.000.03
data.sample.MultiSet000
dumpPackTxt0.010.000.01
esApply1.550.001.55
getPkgVigs000
isCurrent0.030.000.03
isUnique0.020.000.01
isVersioned000
lcSuffix0.000.010.02
listLen000
makeDataPackage0.070.000.08
matchpt0.020.000.01
multiassign000
note000
openPDF000
openVignette000
package.version000
read.AnnotatedDataFrame0.010.000.02
read.MIAME000
readExpressionSet0.070.020.08
reverseSplit000
rowMedians0.040.000.04
rowQ0.020.010.03
selectChannels0.050.000.05
selectSome000
strbreak000
subListExtract1.090.021.11
testBioCConnection0.180.030.57
updateOldESet000
validMsg000

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

nameusersystemelapsed
Aggregate000
ScalarObject-class000
addVig2Menu000
anyMissing000
cache0.010.000.02
channel0.130.000.12
channelNames0.060.000.07
class.AnnotatedDataFrame0.030.000.03
class.ExpressionSet0.280.000.28
class.MIAxE0.020.000.01
class.MultiSet0.040.000.05
class.NChannelSet0.240.000.24
class.Versioned0.080.000.07
class.VersionedBiobase0.010.000.02
class.Versions000
class.VersionsNull000
class.container000
class.eSet0.110.000.11
classVersion000
contents000
copyEnv000
copySubstitute0.020.020.03
createPackage0.000.010.02
data.aaMap000
data.geneData0.030.000.03
data.reporter000
data.sample.ExpressionSet0.020.000.02
data.sample.MultiSet000
dumpPackTxt0.020.000.01
esApply1.620.001.63
getPkgVigs000
isCurrent0.050.000.05
isUnique000
isVersioned0.020.000.01
lcSuffix000
listLen000
makeDataPackage0.080.000.08
matchpt000
multiassign000
note0.010.000.01
openPDF000
openVignette000
package.version000
read.AnnotatedDataFrame0.020.000.02
read.MIAME000
readExpressionSet0.140.000.14
reverseSplit000
rowMedians0.060.000.06
rowQ0.020.000.02
selectChannels0.060.000.06
selectSome000
strbreak000
subListExtract1.030.021.04
testBioCConnection0.110.030.33
updateOldESet000
validMsg000