BioC 3.1: CHECK report for gdsfmt on petty
This page was generated on 2015-10-09 09:37:14 -0700 (Fri, 09 Oct 2015).
gdsfmt 1.4.0
Xiuwen Zheng
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/gdsfmt | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: gdsfmt |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.4.0.tar.gz |
| StartedAt: 2015-10-08 23:07:22 -0700 (Thu, 08 Oct 2015) |
| EndedAt: 2015-10-08 23:09:46 -0700 (Thu, 08 Oct 2015) |
| EllapsedTime: 144.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gdsfmt.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/gdsfmt.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.4.0’
* 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 ... [89s/90s] 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 ... [2s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [19s/20s]
[20s/20s] 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
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
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-3.1-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)
gdsfmt.Rcheck/gdsfmt-Ex.timings:
| name | user | system | elapsed
|
| add.gdsn | 0.088 | 0.012 | 0.100 |
|
| addfile.gdsn | 0.008 | 0.003 | 0.015 |
|
| addfolder.gdsn | 0.030 | 0.006 | 0.036 |
|
| append.gdsn | 0.022 | 0.003 | 0.026 |
|
| apply.gdsn | 0.054 | 0.013 | 0.068 |
|
| assign.gdsn | 0.010 | 0.001 | 0.011 |
|
| cache.gdsn | 0.004 | 0.001 | 0.009 |
|
| cleanup.gds | 0.014 | 0.005 | 0.019 |
|
| closefn.gds | 0.003 | 0.001 | 0.004 |
|
| clusterApply.gdsn | 0.094 | 0.014 | 1.210 |
|
| cnt.gdsn | 0.005 | 0.001 | 0.007 |
|
| compression.gdsn | 0.004 | 0.002 | 0.006 |
|
| createfn.gds | 0.011 | 0.001 | 0.013 |
|
| delete.attr.gdsn | 0.007 | 0.001 | 0.013 |
|
| delete.gdsn | 0.009 | 0.001 | 0.011 |
|
| diagnosis.gds | 0.031 | 0.004 | 0.043 |
|
| gdsfmt-package | 0.041 | 0.005 | 0.048 |
|
| get.attr.gdsn | 0.005 | 0.001 | 0.016 |
|
| getfile.gdsn | 0.007 | 0.003 | 0.013 |
|
| index.gdsn | 0.014 | 0.002 | 0.017 |
|
| is.element.gdsn | 0.006 | 0.002 | 0.008 |
|
| lasterr.gds | 0.001 | 0.000 | 0.001 |
|
| ls.gdsn | 0.005 | 0.001 | 0.016 |
|
| moveto.gdsn | 0.036 | 0.004 | 0.039 |
|
| name.gdsn | 0.005 | 0.002 | 0.007 |
|
| objdesp.gdsn | 0.021 | 0.003 | 0.023 |
|
| openfn.gds | 0.010 | 0.002 | 0.020 |
|
| print.gds.class | 0.003 | 0.001 | 0.005 |
|
| print.gdsn.class | 0.045 | 0.002 | 0.046 |
|
| put.attr.gdsn | 0.006 | 0.002 | 0.019 |
|
| read.gdsn | 0.021 | 0.004 | 0.025 |
|
| readex.gdsn | 0.008 | 0.003 | 0.010 |
|
| readmode.gdsn | 0.007 | 0.002 | 0.014 |
|
| rename.gdsn | 0.006 | 0.002 | 0.014 |
|
| setdim.gdsn | 0.005 | 0.002 | 0.008 |
|
| showfile.gds | 0.007 | 0.001 | 0.014 |
|
| sync.gds | 0.005 | 0.002 | 0.007 |
|
| system.gds | 0.014 | 0.002 | 0.015 |
|
| write.gdsn | 0.005 | 0.002 | 0.008 |
|