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Package 126/479HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.5.19
Simon Anders
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq
Last Changed Rev: 56486 / Revision: 56603
Last Changed Date: 2011-07-01 01:46:33 -0700 (Fri, 01 Jul 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DESeq
Version: 1.5.19
Command: mkdir DESeq.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DESeq.buildbin-libdir DESeq_1.5.19.tar.gz >DESeq-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=DESeq.buildbin-libdir --install="check:DESeq-install.out" --force-multiarch --no-vignettes --timings DESeq_1.5.19.tar.gz && mv DESeq.buildbin-libdir/* DESeq.Rcheck/ && rmdir DESeq.buildbin-libdir
StartedAt: 2011-07-07 04:47:01 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:50:57 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 235.9 seconds
RetCode: 0
Status:  OK  
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/DESeq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DESeq/DESCRIPTION' ... OK
* this is package 'DESeq' version '1.5.19'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DESeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

DESeq.Rcheck/00install.out:


install for i386

* installing *source* package 'DESeq' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength'
gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/i386
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DESeq.Rnw' 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 

add DLL for x64

* installing *source* package 'DESeq' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/x64
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
* MD5 sums
packaged installation of 'DESeq' as DESeq_1.5.19.zip

* DONE (DESeq)

DESeq.Rcheck/DESeq-Ex.timings:

nameusersystemelapsed
CountDataSet-class000
adjustScvForBias0.560.000.56
conditions2.900.022.91
counts2.700.012.72
dispTable4.040.004.04
estimateDispersions4.520.004.52
estimateSizeFactors2.970.002.97
estimateSizeFactorsForMatrix2.590.002.59
fitNbinomGLMs000
fitNbinomGLMsForMatrix000
getBaseMeansAndVariances2.630.002.63
getVarianceStabilizedData4.140.004.14
makeExampleCountDataSet2.570.002.57
nbinomGLMTest3.820.003.82
nbinomTest13.01 0.0013.01
nbinomTestForMatrices22.98 0.0023.01
newCountDataSet2.930.002.93
sizeFactors2.680.002.69