BioC 3.1: CHECK report for gdsfmt on zin2

Package: gdsfmt

Version: 1.4.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings gdsfmt_1.4.0.tar.gz

StartedAt: 2015-10-09 01:30:19 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:33:04 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 165.6 seconds

RetCode: 0

Status:  OK

CheckDir: gdsfmt.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings gdsfmt_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/gdsfmt.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.4.0’
* 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 ... [85s/119s] OK
* checking installed package size ... NOTE
  installed size is 18.0Mb
  sub-directories of 1Mb or more:
    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’ [10s/18s]
 [10s/19s] 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-3.1-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

* installing *source* package ‘gdsfmt’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -Wall -c CoreGDS.cpp -o CoreGDS.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o gdsfmt.so CoreGDS.o 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-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.044	0.004	0.059
addfile.gdsn	0.005	0.000	0.005
addfolder.gdsn	0.014	0.004	0.033
append.gdsn	0.013	0.000	0.031
apply.gdsn	0.020	0.008	0.062
assign.gdsn	0.006	0.000	0.011
cache.gdsn	0.002	0.001	0.005
cleanup.gds	0.004	0.003	0.012
closefn.gds	0.001	0.000	0.011
clusterApply.gdsn	0.039	0.011	1.058
cnt.gdsn	0.003	0.000	0.021
compression.gdsn	0.003	0.000	0.005
createfn.gds	0.006	0.000	0.011
delete.attr.gdsn	0.003	0.000	0.006
delete.gdsn	0.005	0.001	0.005
diagnosis.gds	0.016	0.000	0.028
gdsfmt-package	0.025	0.000	0.060
get.attr.gdsn	0.003	0.000	0.006
getfile.gdsn	0.005	0.000	0.008
index.gdsn	0.007	0.000	0.020
is.element.gdsn	0.005	0.000	0.011
lasterr.gds	0.001	0.000	0.000
ls.gdsn	0.002	0.000	0.004
moveto.gdsn	0.013	0.004	0.037
name.gdsn	0.002	0.000	0.008
objdesp.gdsn	0.010	0.000	0.024
openfn.gds	0.005	0.000	0.005
print.gds.class	0.003	0.000	0.010
print.gdsn.class	0.004	0.000	0.012
put.attr.gdsn	0.003	0.000	0.006
read.gdsn	0.013	0.000	0.023
readex.gdsn	0.005	0.000	0.010
readmode.gdsn	0.002	0.003	0.006
rename.gdsn	0.003	0.000	0.011
setdim.gdsn	0.003	0.000	0.011
showfile.gds	0.003	0.000	0.016
sync.gds	0.001	0.004	0.007
system.gds	0.006	0.000	0.007
write.gdsn	0.002	0.003	0.015