BioC 3.2: CHECK report for gdsfmt on zin1

Package: gdsfmt

Version: 1.6.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gdsfmt_1.6.2.tar.gz

StartedAt: 2016-04-23 00:52:36 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:58:46 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 369.5 seconds

RetCode: 0

Status:  OK

CheckDir: gdsfmt.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gdsfmt_1.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.2’
* 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 ... [90s/90s] OK
* checking installed package size ... NOTE
  installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  16.7Mb
* 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’ [222s/260s]
 [223s/261s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

* installing *source* package ‘gdsfmt’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c R_CoreArray.cpp -o R_CoreArray.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c gdsfmt.cpp -o gdsfmt.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dAny.cpp -o CoreArray/dAny.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dBase.cpp -o CoreArray/dBase.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dFile.cpp -o CoreArray/dFile.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dStream.cpp -o CoreArray/dStream.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/adler32.c -o ZLIB/adler32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/compress.c -o ZLIB/compress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/crc32.c -o ZLIB/crc32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/deflate.c -o ZLIB/deflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/infback.c -o ZLIB/infback.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/inffast.c -o ZLIB/inffast.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/inflate.c -o ZLIB/inflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/inftrees.c -o ZLIB/inftrees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/trees.c -o ZLIB/trees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/uncompr.c -o ZLIB/uncompr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c ZLIB/zutil.c -o ZLIB/zutil.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c LZ4/lz4.c -o LZ4/lz4.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c LZ4/lz4hc.c -o LZ4/lz4hc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c LZ4/lz4frame.c -o LZ4/lz4frame.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c LZ4/xxhash.c -o LZ4/xxhash.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/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 -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	0.093	0.004	0.107
addfile.gdsn	0.009	0.000	0.016
addfolder.gdsn	0.030	0.000	0.029
append.gdsn	0.014	0.004	0.024
apply.gdsn	0.039	0.000	0.053
assign.gdsn	0.025	0.000	0.029
cache.gdsn	0.003	0.000	0.009
cleanup.gds	0.013	0.000	0.018
closefn.gds	0.002	0.000	0.006
clusterApply.gdsn	0.053	0.001	0.641
cnt.gdsn	0.002	0.000	0.011
compression.gdsn	0.005	0.004	0.016
copyto.gdsn	0.041	0.004	0.053
createfn.gds	0.007	0.000	0.011
delete.attr.gdsn	0.005	0.000	0.018
delete.gdsn	0.006	0.004	0.016
diagnosis.gds	0.004	0.004	0.008
gdsfmt-package	0.037	0.000	0.044
get.attr.gdsn	0.004	0.000	0.009
getfile.gdsn	0.035	0.000	0.035
getfolder.gdsn	0.030	0.000	0.038
index.gdsn	0.012	0.000	0.017
is.element.gdsn	0.004	0.000	0.008
lasterr.gds	0	0	0
ls.gdsn	0.002	0.000	0.006
moveto.gdsn	0.033	0.000	0.039
name.gdsn	0.004	0.000	0.007
objdesp.gdsn	0.012	0.000	0.017
openfn.gds	0.004	0.004	0.008
permdim.gdsn	0.013	0.000	0.018
print.gds.class	0.009	0.000	0.013
put.attr.gdsn	0.006	0.000	0.011
read.gdsn	0.018	0.000	0.022
readex.gdsn	0.011	0.000	0.016
readmode.gdsn	0.004	0.000	0.008
rename.gdsn	0.006	0.000	0.010
setdim.gdsn	0.012	0.000	0.023
showfile.gds	0.007	0.000	0.019
sync.gds	0.004	0.000	0.009
system.gds	0.008	0.000	0.008
write.gdsn	0.004	0.000	0.014