oligo 1.30.0
Benilton Carvalho
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/oligo | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### rm -rf oligo.buildbin-libdir oligo.Rcheck && mkdir oligo.buildbin-libdir oligo.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligo.buildbin-libdir oligo_1.30.0.tar.gz >oligo.Rcheck\00install.out 2>&1 && cp oligo.Rcheck\00install.out oligo-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=oligo.buildbin-libdir --install="check:oligo-install.out" --force-multiarch --no-vignettes --timings oligo_1.30.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/oligo.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.30.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'oligo' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocGenerics' 'ff'
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
Unexported object imported by a ':::' call: 'Biobase:::annotatedDataFrameFromMatrix'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
.Call("read_abatch", ..., PACKAGE = "affyio")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for 'getBar'
availProbeInfo: no visible global function definition for
'dbListFields'
basicPLM: no visible global function definition for 'createFF'
basicRMAbo: no visible global function definition for 'createFF'
cloneFS: no visible global function definition for 'ldPath'
computeDABG: no visible global function definition for 'createFF'
ffSubset: no visible global function definition for 'createFF'
fitAffySnpMixture2: no visible global function definition for
'ldStatus'
fitAffySnpMixture2: no visible global function definition for
'createFF'
fitAffySnpMixture2: no visible global function definition for 'ldPath'
getFidMetaProbesetCore: no visible global function definition for
'dbDisconnect'
getFidMetaProbesetExtended: no visible global function definition for
'dbDisconnect'
getFidMetaProbesetFull: no visible global function definition for
'dbDisconnect'
getFidProbeset: no visible global function definition for
'dbDisconnect'
read.celfiles: no visible global function definition for
'varMetadata<-'
read.xysfiles: no visible global function definition for
'varMetadata<-'
rmaBgCorrectLDSmaster: no visible global function definition for
'ldStatus'
rmaBgCorrectLDSmaster: no visible global function definition for
'ldPath'
smartReadCEL: no visible global function definition for 'createFF'
smartReadXYS: no visible global function definition for 'createFF'
normalize,ff_matrix: no visible global function definition for 'ldPath'
normalizeToTarget,ff_matrix: no visible global function definition for
'ldPath'
runDate,FeatureSet: no visible global function definition for
'varLabels'
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* 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-3.0-bioc/meat/oligo.buildbin-libdir/oligo/libs/i386/oligo.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64/oligo.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [161s] WARNING
Found the following significant warnings:
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessTools 36.75 0.54 37.66
getProbeInfo 17.65 0.41 68.81
read.celfiles 5.85 0.13 13.69
fitProbeLevelModel 5.79 0.06 7.07
IntensityMatrix-methods 2.60 0.01 5.46
** running examples for arch 'x64' ... [103s] WARNING
Found the following significant warnings:
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessTools 39.92 0.43 40.35
getProbeInfo 18.71 0.35 19.05
fitProbeLevelModel 6.11 0.09 6.21
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRUnit.R' [319s]
[319s] OK
** running tests for arch 'x64' ...
Running 'doRUnit.R' [170s]
[171s] OK
* checking PDF version of manual ... OK
* DONE
WARNING: There were 3 warnings.
NOTE: There were 6 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/oligo.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'oligo' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3˜1.0-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lRblas -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-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
** testing if installed package can be loaded
install for x64
* installing *source* package 'oligo' ...
** libs
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-bioc/R/library/preprocessCore/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.0-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-3˜1.0-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lRblas -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligo' as oligo_1.30.0.zip
* DONE (oligo)