BioC 3.2: CHECK report for gdsfmt on perceval

Package: gdsfmt

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.6.1.tar.gz

StartedAt: 2015-10-27 08:02:32 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:09:41 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 429.2 seconds

RetCode: 0

Status:  OK

CheckDir: gdsfmt.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.6.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gdsfmt’ can be installed ... [66s/69s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
* 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 ... 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [316s/333s]
 [316s/333s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘gdsfmt’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_CoreArray.cpp -o R_CoreArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gdsfmt.cpp -o gdsfmt.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/adler32.c -o ZLIB/adler32.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/compress.c -o ZLIB/compress.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/crc32.c -o ZLIB/crc32.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/deflate.c -o ZLIB/deflate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/infback.c -o ZLIB/infback.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inffast.c -o ZLIB/inffast.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inflate.c -o ZLIB/inflate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/trees.c -o ZLIB/trees.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/zutil.c -o ZLIB/zutil.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4.c -o LZ4/lz4.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
LZ4/lz4.c:153: warning: ‘LZ4_readLE16’ defined but not used
LZ4/lz4.c:202: warning: ‘LZ4_copy4’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/xxhash.c -o LZ4/xxhash.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o gdsfmt.so R_CoreArray.o gdsfmt.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dSerial.o CoreArray/dStream.o CoreArray/dStruct.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck/gdsfmt/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gdsfmt)

name	user	system	elapsed
add.gdsn	0.119	0.010	0.130
addfile.gdsn	0.009	0.002	0.015
addfolder.gdsn	0.036	0.004	0.041
append.gdsn	0.024	0.003	0.027
apply.gdsn	0.042	0.010	0.052
assign.gdsn	0.029	0.006	0.035
cache.gdsn	0.004	0.001	0.004
cleanup.gds	0.014	0.002	0.018
closefn.gds	0.002	0.000	0.002
clusterApply.gdsn	0.068	0.011	0.820
cnt.gdsn	0.003	0.001	0.003
compression.gdsn	0.008	0.001	0.016
copyto.gdsn	0.057	0.002	0.059
createfn.gds	0.008	0.001	0.022
delete.attr.gdsn	0.006	0.001	0.008
delete.gdsn	0.009	0.002	0.022
diagnosis.gds	0.010	0.002	0.017
gdsfmt-package	0.043	0.004	0.048
get.attr.gdsn	0.005	0.001	0.006
getfile.gdsn	0.043	0.002	0.045
getfolder.gdsn	0.035	0.005	0.040
index.gdsn	0.015	0.003	0.018
is.element.gdsn	0.003	0.001	0.007
lasterr.gds	0.000	0.000	0.001
ls.gdsn	0.002	0.001	0.003
moveto.gdsn	0.040	0.003	0.042
name.gdsn	0.003	0.001	0.004
objdesp.gdsn	0.014	0.002	0.024
openfn.gds	0.009	0.002	0.013
permdim.gdsn	0.015	0.004	0.019
print.gds.class	0.010	0.001	0.013
put.attr.gdsn	0.006	0.001	0.008
read.gdsn	0.024	0.003	0.027
readex.gdsn	0.013	0.004	0.017
readmode.gdsn	0.004	0.001	0.007
rename.gdsn	0.007	0.001	0.007
setdim.gdsn	0.013	0.003	0.022
showfile.gds	0.006	0.001	0.008
sync.gds	0.004	0.001	0.005
system.gds	0.012	0.001	0.013
write.gdsn	0.004	0.002	0.009