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BioC 2.12: CHECK report for DESeq on moscato2

This page was generated on 2013-10-09 09:38:44 -0700 (Wed, 09 Oct 2013).

Package 176/671HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq 1.12.1
Simon Anders
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DESeq
Last Changed Rev: 79715 / Revision: 81334
Last Changed Date: 2013-08-22 03:51:42 -0700 (Thu, 22 Aug 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: DESeq
Version: 1.12.1
Command: rm -rf DESeq.buildbin-libdir && mkdir DESeq.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DESeq.buildbin-libdir DESeq_1.12.1.tar.gz >DESeq-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=DESeq.buildbin-libdir --install="check:DESeq-install.out" --force-multiarch --no-vignettes --timings DESeq_1.12.1.tar.gz && mv DESeq.buildbin-libdir/* DESeq.Rcheck/ && rmdir DESeq.buildbin-libdir
StartedAt: 2013-10-09 01:49:53 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:57:10 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 437.1 seconds
RetCode: 0
Status:  OK  
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/DESeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DESeq/DESCRIPTION' ... OK
* this is package 'DESeq' version '1.12.1'
* 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 'DESeq' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... NOTE
plotMA: no visible binding for global variable 'baseMean'
* 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 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-2.12-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/i386/DESeq.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/x64/DESeq.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.  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' ... NOTE
The following files should probably not be installed:
  'whbiocvignette.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [135s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
nbinomTestForMatrices 53.11      0   53.11
nbinomTest            27.02      0   27.02
** running examples for arch 'x64' ... [129s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
nbinomTestForMatrices 44.75      0   44.77
nbinomTest            24.47      0   24.47
plotPCA                5.63      0    5.63
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/DESeq.Rcheck/00check.log'
for details.

DESeq.Rcheck/00install.out:


install for i386

* installing *source* package 'DESeq' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
gcc -m32 -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/i386
** R
** 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 'DESeq' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o DESeq.dll tmp.def pval.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/DESeq.buildbin-libdir/DESeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DESeq' as DESeq_1.12.1.zip
* DONE (DESeq)