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BioC 3.0: CHECK report for gdsfmt on perceval

This page was generated on 2015-04-10 10:00:49 -0700 (Fri, 10 Apr 2015).

Package 340/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.2.2
Xiuwen Zheng
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/gdsfmt
Last Changed Rev: 98410 / Revision: 102249
Last Changed Date: 2015-01-16 13:00:05 -0800 (Fri, 16 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: gdsfmt
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gdsfmt_1.2.2.tar.gz
StartedAt: 2015-04-10 01:47:43 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:49:21 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 98.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gdsfmt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gdsfmt_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/gdsfmt.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.2.2’
* 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 ... [64s/66s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘parallel’ ‘RUnit’
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/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 was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

gdsfmt.Rcheck/00install.out:

* 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 CoreGDS.cpp -o CoreGDS.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 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:188: warning: ‘LZ4_readLE16’ defined but not used
LZ4/lz4.c:260: 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
LZ4/lz4frame.c: In function ‘LZ4F_compressFrameBound’:
LZ4/lz4frame.c:222: warning: missing braces around initializer
LZ4/lz4frame.c:222: warning: (near initialization for ‘prefs.frameInfo’)
LZ4/lz4frame.c: In function ‘LZ4F_compressFrame’:
LZ4/lz4frame.c:261: warning: missing braces around initializer
LZ4/lz4frame.c:261: warning: (near initialization for ‘cctxI.prefs’)
LZ4/lz4frame.c:262: warning: missing braces around initializer
LZ4/lz4frame.c:262: warning: (near initialization for ‘prefs.frameInfo’)
LZ4/lz4frame.c: In function ‘LZ4F_compressBegin’:
LZ4/lz4frame.c:364: warning: missing braces around initializer
LZ4/lz4frame.c:364: warning: (near initialization for ‘prefNull.frameInfo’)
LZ4/lz4frame.c: In function ‘LZ4F_compressBound’:
LZ4/lz4frame.c:439: warning: missing braces around initializer
LZ4/lz4frame.c:439: warning: (near initialization for ‘prefsNull.frameInfo’)
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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/nm: no name list
installing to /Users/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)

gdsfmt.Rcheck/gdsfmt-Ex.timings:

nameusersystemelapsed
add.gdsn0.0640.0120.101
addfile.gdsn0.0090.0040.033
addfolder.gdsn0.0250.0060.049
append.gdsn0.0190.0030.028
apply.gdsn0.0430.0130.082
assign.gdsn0.0080.0010.014
cache.gdsn0.0020.0010.016
cleanup.gds0.0130.0040.042
closefn.gds0.0020.0010.012
clusterApply.gdsn0.0700.0160.986
cnt.gdsn0.0030.0020.009
compression.gdsn0.0040.0020.024
createfn.gds0.0090.0020.020
delete.attr.gdsn0.0050.0020.018
delete.gdsn0.0060.0020.014
diagnosis.gds0.0130.0050.042
gdsfmt-package0.0370.0060.059
get.attr.gdsn0.0040.0010.018
getfile.gdsn0.0090.0030.033
index.gdsn0.0100.0020.021
is.element.gdsn0.0050.0030.014
lasterr.gds0.0000.0000.001
ls.gdsn0.0040.0020.016
moveto.gdsn0.0820.0040.091
name.gdsn0.0050.0030.015
objdesp.gdsn0.0150.0030.028
openfn.gds0.0080.0020.024
print.gds.class0.0030.0010.018
print.gdsn.class0.0050.0020.022
put.attr.gdsn0.0050.0020.014
read.gdsn0.0160.0030.027
readex.gdsn0.0060.0020.019
readmode.gdsn0.0040.0020.014
rename.gdsn0.0050.0020.015
setdim.gdsn0.0050.0020.014
showfile.gds0.0070.0030.014
sync.gds0.0090.0030.020
system.gds0.0180.0020.020
write.gdsn0.0050.0020.011