oligo 1.28.3
Benilton Carvalho
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/oligo | | Last Changed Rev: 94433 / Revision: 95116 | | Last Changed Date: 2014-09-23 10:38:51 -0700 (Tue, 23 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligo_1.28.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/oligo.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.28.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘oligo’ can be installed ... [29s/36s] 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
* 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("read_abatch", ..., PACKAGE = "affyio")
.Call("ReadHeader", ..., 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [134s/142s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessTools 43.328 1.846 47.971
getProbeInfo 29.023 1.293 31.889
fitProbeLevelModel 10.370 0.266 12.336
rma-methods 7.187 0.131 7.715
read.celfiles 6.834 0.429 7.848
MAplot-methods 5.237 0.099 5.781
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’ [273s/309s]
[274s/310s] OK
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/oligo.Rcheck/00check.log’
for details.
* installing *source* package ‘oligo’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c DABG.c -o DABG.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c ParserGzXYS.c -o ParserGzXYS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c baseProfile.c -o baseProfile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c basecontent.c -o basecontent.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c chipbackground.c -o chipbackground.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c mas5calls.c -o mas5calls.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c rma2.c -o rma2.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c rma_common.c -o rma_common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include" -fPIC -mtune=core2 -g -O2 -Wall -c trimmed.c -o trimmed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/oligo.Rcheck/oligo/libs
** 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"
in method for ‘rma’ with signature ‘"HTAFeatureSet"’: no definition for class “HTAFeatureSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligo)