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Package 415/609HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.22.0
Benilton Carvalho
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/oligo
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: oligo
Version: 1.22.0
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligo.buildbin-libdir oligo_1.22.0.tar.gz >oligo-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=oligo.buildbin-libdir --install="check:oligo-install.out" --force-multiarch --no-vignettes --timings oligo_1.22.0.tar.gz && mv oligo.buildbin-libdir/* oligo.Rcheck/ && rmdir oligo.buildbin-libdir
StartedAt: 2013-03-25 02:18:44 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:32:59 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 855.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: oligo.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/oligo.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking: 'doMC' 'doMPI'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'oligo' can be installed ... WARNING
Found the following significant warnings:
  D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
See 'D:/biocbld/bbs-2.11-bioc/meat/oligo.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    scripts   2.7Mb
* checking package directory ... OK
* checking for portable file names ... 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 ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_abatch", ..., PACKAGE = "affyio")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* 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 compilation flags in Makevars ... 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 'D:/biocbld/bbs-2.11-bioc/meat/oligo.buildbin-libdir/oligo/libs/i386/oligo.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.11-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64/oligo.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call functions 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
preprocessTools    34.96   0.56   36.05
getProbeInfo       18.95   0.50   47.88
read.celfiles       7.49   0.22   14.49
fitProbeLevelModel  7.08   0.03    7.38
rma-methods         5.37   0.08    5.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
preprocessTools    34.92   0.46   35.52
getProbeInfo       19.59   0.60   20.22
fitProbeLevelModel  7.25   0.08    7.36
read.celfiles       5.67   0.39    6.07
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64'
  Running 'doRUnit.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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.11-bioc/meat/oligo.Rcheck/00check.log'
for details.

oligo.Rcheck/00install.out:


install for i386

* installing *source* package 'oligo' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
In file included from baseProfile.c:4:0:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
gcc -m32 -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lRlapack -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lRblas -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/oligo.buildbin-libdir/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
Note: in method for 'pm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for 'mm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
   'primer.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'oligo' ...
** libs
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
In file included from baseProfile.c:4:0:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
gcc -m64 -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lRblas -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligo' as oligo_1.22.0.zip

* DONE (oligo)