BioC 3.0: CHECK report for gdsfmt on zin1

Package: gdsfmt

Version: 1.2.2

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings gdsfmt_1.2.2.tar.gz

StartedAt: 2015-04-10 00:11:32 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:13:14 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 102.6 seconds

RetCode: 0

Status: OK

CheckDir: gdsfmt.Rcheck

Warnings: 0

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###
### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings gdsfmt_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/gdsfmt.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.2.2’
* 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 ... [74s/76s] OK
* checking installed package size ... NOTE
  installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘RUnit’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [0s/1s]
 [1s/1s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

* installing *source* package ‘gdsfmt’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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	0.088	0.000	0.090
addfile.gdsn	0.004	0.004	0.121
addfolder.gdsn	0.016	0.012	0.031
append.gdsn	0.020	0.004	0.023
apply.gdsn	0.044	0.008	0.052
assign.gdsn	0.012	0.004	0.012
cache.gdsn	0.000	0.004	0.004
cleanup.gds	0.016	0.000	0.013
closefn.gds	0.004	0.000	0.002
clusterApply.gdsn	0.048	0.004	0.652
cnt.gdsn	0.004	0.000	0.003
compression.gdsn	0.004	0.000	0.004
createfn.gds	0.008	0.000	0.005
delete.attr.gdsn	0.004	0.000	0.004
delete.gdsn	0.008	0.000	0.006
diagnosis.gds	0.012	0.000	0.010
gdsfmt-package	0.028	0.000	0.030
get.attr.gdsn	0.000	0.000	0.003
getfile.gdsn	0.004	0.000	3.709
index.gdsn	0.008	0.000	0.017
is.element.gdsn	0.004	0.000	0.004
lasterr.gds	0.000	0.000	0.001
ls.gdsn	0.004	0.000	0.003
moveto.gdsn	0.016	0.004	0.020
name.gdsn	0.000	0.000	0.003
objdesp.gdsn	0.008	0.000	0.011
openfn.gds	0.004	0.000	0.006
print.gds.class	0.004	0.000	0.003
print.gdsn.class	0.008	0.000	0.005
put.attr.gdsn	0.004	0.000	0.004
read.gdsn	0.012	0.000	0.013
readex.gdsn	0.004	0.000	0.006
readmode.gdsn	0.004	0.000	0.002
rename.gdsn	0.000	0.000	0.003
setdim.gdsn	0.004	0.000	0.004
showfile.gds	0.004	0.000	0.004
sync.gds	0.000	0.004	0.004
system.gds	0.008	0.000	0.010
write.gdsn	0.008	0.000	0.004

BioC 3.0: CHECK report for gdsfmt on zin1

Summary

Command output