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BioC 3.5: CHECK report for gdsfmt on veracruz2

This page was generated on 2017-08-16 13:32:48 -0400 (Wed, 16 Aug 2017).

Package 500/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.12.0
Xiuwen Zheng
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/gdsfmt
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gdsfmt
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.12.0.tar.gz
StartedAt: 2017-08-16 03:05:28 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:11:29 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 360.2 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 gdsfmt_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gdsfmt.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

gdsfmt.Rcheck/00install.out:

* installing *source* package ‘gdsfmt’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_CoreArray.cpp -o R_CoreArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c gdsfmt.cpp -o gdsfmt.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c digest.cpp -o digest.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/adler32.c -o ZLIB/adler32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/compress.c -o ZLIB/compress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/crc32.c -o ZLIB/crc32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/deflate.c -o ZLIB/deflate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/infback.c -o ZLIB/infback.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/inffast.c -o ZLIB/inffast.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/inflate.c -o ZLIB/inflate.o
ZLIB/inflate.c:1507:61: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
    if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16;
                                                        ˜˜˜ ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/trees.c -o ZLIB/trees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/zutil.c -o ZLIB/zutil.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/lz4.c -o LZ4/lz4.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && tar -xzf xz-5.2.3.tar.gz
cd XZ/xz-5.2.3 && \
		./configure CC="clang" CPP="clang -E" CXX="clang++ " CXXCPP="clang++  -E" --build="" --with-pic --enable-silent-rules --quiet > /dev/null
cd XZ/xz-5.2.3/src/liblzma && make
Making all in api
make[2]: Nothing to be done for `all'.
  CC       liblzma_la-tuklib_physmem.lo
  CC       liblzma_la-tuklib_cpucores.lo
  CC       liblzma_la-common.lo
  CC       liblzma_la-block_util.lo
  CC       liblzma_la-easy_preset.lo
  CC       liblzma_la-filter_common.lo
  CC       liblzma_la-hardware_physmem.lo
  CC       liblzma_la-index.lo
  CC       liblzma_la-stream_flags_common.lo
  CC       liblzma_la-vli_size.lo
  CC       liblzma_la-hardware_cputhreads.lo
  CC       liblzma_la-alone_encoder.lo
  CC       liblzma_la-block_buffer_encoder.lo
  CC       liblzma_la-block_encoder.lo
  CC       liblzma_la-block_header_encoder.lo
  CC       liblzma_la-easy_buffer_encoder.lo
  CC       liblzma_la-easy_encoder.lo
  CC       liblzma_la-easy_encoder_memusage.lo
  CC       liblzma_la-filter_buffer_encoder.lo
  CC       liblzma_la-filter_encoder.lo
  CC       liblzma_la-filter_flags_encoder.lo
  CC       liblzma_la-index_encoder.lo
  CC       liblzma_la-stream_buffer_encoder.lo
  CC       liblzma_la-stream_encoder.lo
  CC       liblzma_la-stream_flags_encoder.lo
  CC       liblzma_la-vli_encoder.lo
  CC       liblzma_la-outqueue.lo
  CC       liblzma_la-stream_encoder_mt.lo
  CC       liblzma_la-alone_decoder.lo
  CC       liblzma_la-auto_decoder.lo
  CC       liblzma_la-block_buffer_decoder.lo
  CC       liblzma_la-block_decoder.lo
  CC       liblzma_la-block_header_decoder.lo
  CC       liblzma_la-easy_decoder_memusage.lo
  CC       liblzma_la-filter_buffer_decoder.lo
  CC       liblzma_la-filter_decoder.lo
  CC       liblzma_la-filter_flags_decoder.lo
  CC       liblzma_la-index_decoder.lo
  CC       liblzma_la-index_hash.lo
  CC       liblzma_la-stream_buffer_decoder.lo
  CC       liblzma_la-stream_decoder.lo
  CC       liblzma_la-stream_flags_decoder.lo
  CC       liblzma_la-vli_decoder.lo
  CC       liblzma_la-check.lo
  CC       liblzma_la-crc32_table.lo
  CC       liblzma_la-crc32_fast.lo
  CC       liblzma_la-crc64_table.lo
  CC       liblzma_la-crc64_fast.lo
  CC       liblzma_la-sha256.lo
  CC       liblzma_la-lz_encoder.lo
  CC       liblzma_la-lz_encoder_mf.lo
  CC       liblzma_la-lz_decoder.lo
  CC       liblzma_la-lzma_encoder_presets.lo
  CC       liblzma_la-lzma_encoder.lo
  CC       liblzma_la-lzma_encoder_optimum_fast.lo
  CC       liblzma_la-lzma_encoder_optimum_normal.lo
  CC       liblzma_la-fastpos_table.lo
  CC       liblzma_la-lzma_decoder.lo
  CC       liblzma_la-lzma2_encoder.lo
  CC       liblzma_la-lzma2_decoder.lo
  CC       liblzma_la-price_table.lo
  CC       liblzma_la-delta_common.lo
  CC       liblzma_la-delta_encoder.lo
  CC       liblzma_la-delta_decoder.lo
  CC       liblzma_la-simple_coder.lo
  CC       liblzma_la-simple_encoder.lo
  CC       liblzma_la-simple_decoder.lo
  CC       liblzma_la-x86.lo
  CC       liblzma_la-powerpc.lo
  CC       liblzma_la-ia64.lo
  CC       liblzma_la-arm.lo
  CC       liblzma_la-armthumb.lo
  CC       liblzma_la-sparc.lo
  CCLD     liblzma.la
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
  PC       liblzma.pc
cp XZ/xz-5.2.3/src/liblzma/.libs/liblzma.a .
rm -rf XZ/xz-5.2.3/dos
rm -rf XZ/xz-5.2.3/po
clang++ -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 -o gdsfmt.so R_CoreArray.o gdsfmt.o digest.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 CoreArray/dVLIntGDS.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 liblzma.a -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/gdsfmt.Rcheck/gdsfmt/libs
** R
** inst
** byte-compile and prepare 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.gdsn0.1440.0090.156
addfile.gdsn0.0060.0020.009
addfolder.gdsn0.0220.0030.026
append.gdsn0.0150.0020.017
apply.gdsn0.0410.0090.049
assign.gdsn0.0200.0040.028
cache.gdsn0.0030.0010.004
cleanup.gds0.0120.0020.014
closefn.gds0.0010.0000.001
clusterApply.gdsn0.0390.0090.607
cnt.gdsn0.0030.0010.003
compression.gdsn0.0050.0010.006
copyto.gdsn0.0220.0020.023
createfn.gds0.0060.0010.007
delete.attr.gdsn0.0040.0010.005
delete.gdsn0.0070.0010.009
diagnosis.gds0.0130.0020.015
digest.gdsn0.0480.0070.055
gdsfmt-package0.0310.0040.037
get.attr.gdsn0.0040.0010.004
getfile.gdsn0.0090.0020.011
getfolder.gdsn0.0290.0020.031
index.gdsn0.0140.0010.017
is.element.gdsn0.0030.0020.004
lasterr.gds0.0000.0000.001
ls.gdsn0.0010.0010.003
moveto.gdsn0.0300.0020.032
name.gdsn0.0020.0010.004
objdesp.gdsn0.0100.0020.013
openfn.gds0.0090.0010.010
permdim.gdsn0.0070.0010.008
print.gds.class0.0170.0020.018
put.attr.gdsn0.0050.0010.007
read.gdsn0.0170.0020.020
readex.gdsn0.0100.0030.013
readmode.gdsn0.0030.0010.004
rename.gdsn0.0050.0010.006
setdim.gdsn0.0120.0020.014
showfile.gds0.0050.0010.006
summarize.gdsn0.0030.0010.003
sync.gds0.0040.0010.005
system.gds0.0080.0010.008
write.gdsn0.0030.0020.005