Xiuwen Zheng
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/gdsfmt |
| Branch: RELEASE_3_9 |
| Last Commit: b1fbaba |
| Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:50 -0400 (Wed, 16 Oct 2019).
| Package 616/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gdsfmt 1.20.0 Xiuwen Zheng
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: gdsfmt |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gdsfmt_1.20.0.tar.gz |
| StartedAt: 2019-10-16 02:59:55 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:04:00 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 245.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gdsfmt.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gdsfmt_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.20.0’ * 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 ... 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 ... NOTE Note: information on .o files is not available * 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-3.9-bioc/meat/gdsfmt.Rcheck/00check.log’ for details.
gdsfmt.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gdsfmt
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c gdsfmt.cpp -o gdsfmt.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c digest.cpp -o digest.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dAny.cpp -o CoreArray/dAny.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dBase.cpp -o CoreArray/dBase.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dFile.cpp -o CoreArray/dFile.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dStream.cpp -o CoreArray/dStream.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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++ -std=gnu++11" CXXCPP="clang++ -std=gnu++11 -E" --build="" \
--with-pic --enable-silent-rules --quiet --disable-xz > /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++ -std=gnu++11 -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/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-gdsfmt/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gdsfmt)
gdsfmt.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> options(test.verbose=FALSE)
> BiocGenerics:::testPackage("gdsfmt")
FUNCTION: add.gdsn
FUNCTION: addfile.gdsn
FUNCTION: addfolder.gdsn
FUNCTION: append.gdsn
FUNCTION: apply.gdsn
[1] 1 11 21 31 41 51
[1] 2 12 22 32 42 52
[1] 3 13 23 33 43 53
[1] 4 14 24 34 44 54
[1] 5 15 25 35 45 55
[1] 6 16 26 36 46 56
[1] 7 17 27 37 47 57
[1] 8 18 28 38 48 58
[1] 9 19 29 39 49 59
[1] 10 20 30 40 50 60
[1] 1 21 41
[1] 3 23 43
[1] 5 25 45
[1] 7 27 47
[1] 9 29 49
index: 1, [1] 1 21 41
index: 2, [1] 3 23 43
index: 3, [1] 5 25 45
index: 4, [1] 7 27 47
index: 5, [1] 9 29 49
index: 1, [1] 1 21 41
index: 3, [1] 3 23 43
index: 5, [1] 5 25 45
index: 7, [1] 7 27 47
index: 9, [1] 9 29 49
[1] "L,1" "L,11" "L,21" "L,31" "L,41" "L,51"
[1] "L,2" "L,12" "L,22" "L,32" "L,42" "L,52"
[1] "L,3" "L,13" "L,23" "L,33" "L,43" "L,53"
[1] "L,4" "L,14" "L,24" "L,34" "L,44" "L,54"
[1] "L,5" "L,15" "L,25" "L,35" "L,45" "L,55"
[1] "L,6" "L,16" "L,26" "L,36" "L,46" "L,56"
[1] "L,7" "L,17" "L,27" "L,37" "L,47" "L,57"
[1] "L,8" "L,18" "L,28" "L,38" "L,48" "L,58"
[1] "L,9" "L,19" "L,29" "L,39" "L,49" "L,59"
[1] "L,10" "L,20" "L,30" "L,40" "L,50" "L,60"
[1] 1 2 3 4 5 6 7 8 9 10
[1] 11 12 13 14 15 16 17 18 19 20
[1] 21 22 23 24 25 26 27 28 29 30
[1] 31 32 33 34 35 36 37 38 39 40
[1] 41 42 43 44 45 46 47 48 49 50
[1] 51 52 53 54 55 56 57 58 59 60
[1] 1 3 5 7 9
[1] 21 23 25 27 29
[1] 41 43 45 47 49
[1] "L,1" "L,3" "L,5" "L,7" "L,9"
[1] "L,21" "L,23" "L,25" "L,27" "L,29"
[1] "L,41" "L,43" "L,45" "L,47" "L,49"
[1] 1 11 NA NA 41 51
[1] 2 12 NA NA 42 52
[1] 3 13 NA NA 43 53
[1] 4 14 NA NA 44 54
[1] 5 15 NA NA 45 55
[1] 6 NA NA NA 46 56
[1] 7 NA NA NA 47 57
[1] 8 NA NA NA 48 58
[1] 9 NA NA NA 49 59
[1] 10 NA NA NA 50 60
[1] 1 2 3 4 5 6 7 8 9 10
[1] 11 12 13 14 15 NA NA NA NA NA
[1] NA NA NA NA NA NA NA NA NA NA
[1] NA NA NA NA NA NA NA NA NA NA
[1] 41 42 43 44 45 46 47 48 49 50
[1] 51 52 53 54 55 56 57 58 59 60
$X
[1] 1 11 21 31 41
$Y
[1] 0.01 0.11 0.21 0.31 0.41
$Z
[1] ABC
Levels: ABC DEF ETD TTT
$X
[1] 2 12 22 32 42
$Y
[1] 0.02 0.12 0.22 0.32 0.42
$Z
[1] DEF
Levels: ABC DEF ETD TTT
$X
[1] 3 13 23 33 43
$Y
[1] 0.03 0.13 0.23 0.33 0.43
$Z
[1] ETD
Levels: ABC DEF ETD TTT
$X
[1] 4 14 24 34 44
$Y
[1] 0.04 0.14 0.24 0.34 0.44
$Z
[1] ABC
Levels: ABC DEF ETD TTT
$X
[1] 5 15 25 35 45
$Y
[1] 0.05 0.15 0.25 0.35 0.45
$Z
[1] DEF
Levels: ABC DEF ETD TTT
$X
[1] 6 16 26 36 46
$Y
[1] 0.06 0.16 0.26 0.36 0.46
$Z
[1] ETD
Levels: ABC DEF ETD TTT
$X
[1] 7 17 27 37 47
$Y
[1] 0.07 0.17 0.27 0.37 0.47
$Z
[1] ABC
Levels: ABC DEF ETD TTT
$X
[1] 8 18 28 38 48
$Y
[1] 0.08 0.18 0.28 0.38 0.48
$Z
[1] DEF
Levels: ABC DEF ETD TTT
$X
[1] 9 19 29 39 49
$Y
[1] 0.09 0.19 0.29 0.39 0.49
$Z
[1] ETD
Levels: ABC DEF ETD TTT
$X
[1] 10 20 30 40 50
$Y
[1] 0.1 0.2 0.3 0.4 0.5
$Z
[1] TTT
Levels: ABC DEF ETD TTT
$X
[1] 1 2 3 4 5 6 7 8 9 10
$Y
[1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10
$Z
[1] TRUE
$X
[1] 11 12 13 14 15 16 17 18 19 20
$Y
[1] 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20
$Z
[1] FALSE
$X
[1] 21 22 23 24 25 26 27 28 29 30
$Y
[1] 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30
$Z
[1] TRUE
$X
[1] 31 32 33 34 35 36 37 38 39 40
$Y
[1] 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40
$Z
[1] FALSE
$X
[1] 41 42 43 44 45 46 47 48 49 50
$Y
[1] 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50
$Z
[1] TRUE
$X
[1] 1 2 3 4 5 6 7 8 9 10
$Y
[1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10
$Z
[1] NA
$X
[1] 11 12 13 14 15 16 17 18 19 20
$Y
[1] 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20
$Z
[1] FALSE
$X
[1] 21 22 23 24 25 26 27 28 29 30
$Y
[1] 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30
$Z
[1] NA
$X
[1] 31 32 33 34 NA NA NA NA NA NA
$Y
[1] 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40
$Z
[1] FALSE
$X
[1] NA NA NA NA NA 46 47 48 49 50
$Y
[1] 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50
$Z
[1] NA
$X
[1] 1 2 3 4 5 6 7 8 9 10
$Y
[1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10
$Z
[1] NA
$X
[1] 11 12 13 14 15 16 17 18 19 20
$Y
[1] 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20
$Z
[1] FALSE
$X
[1] 21 22 23 24 25 26 27 28 29 30
$Y
[1] 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30
$Z
[1] NA
$X
[1] 31 32 33 34 NA NA NA NA NA NA
$Y
[1] 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40
$Z
[1] FALSE
$X
[1] NA NA NA NA NA 46 47 48 49 50
$Y
[1] 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50
$Z
[1] NA
$X
[1] 2 22 42
$Y
[1] 0.02 0.22 0.42
$Z
[1] DEF
Levels: ABC DEF ETD TTT
$X
[1] 4 24 44
$Y
[1] 0.04 0.24 0.44
$Z
[1] ABC
Levels: ABC DEF ETD TTT
$X
[1] 6 26 46
$Y
[1] 0.06 0.26 0.46
$Z
[1] ETD
Levels: ABC DEF ETD TTT
$X
[1] 8 28 48
$Y
[1] 0.08 0.28 0.48
$Z
[1] DEF
Levels: ABC DEF ETD TTT
$X
[1] 10 30 50
$Y
[1] 0.1 0.3 0.5
$Z
[1] TTT
Levels: ABC DEF ETD TTT
$X
[1] 2 4 6 8 10
$Y
[1] 0.02 0.04 0.06 0.08 0.10
$Z
[1] TRUE
$X
[1] 22 24 26 28 30
$Y
[1] 0.22 0.24 0.26 0.28 0.30
$Z
[1] TRUE
$X
[1] 42 44 46 48 50
$Y
[1] 0.42 0.44 0.46 0.48 0.50
$Z
[1] TRUE
FUNCTION: assign.gdsn
FUNCTION: cache.gdsn
FUNCTION: cleanup.gds
Clean up the fragments of GDS file:
open the file 'test.gds' (59.5K)
# of fragments: 8
save to 'test.gds.tmp'
rename 'test.gds.tmp' (59.5K, reduced: 12B)
# of fragments: 7
FUNCTION: closefn.gds
FUNCTION: clusterApply.gdsn
FUNCTION: cnt.gdsn
FUNCTION: compression.gdsn
FUNCTION: copyto.gdsn
FUNCTION: createfn.gds
FUNCTION: delete.attr.gdsn
FUNCTION: delete.gdsn
FUNCTION: diagnosis.gds
Clean up the fragments of GDS file:
open the file 'test.gds' (5.2K)
# of fragments: 5
save to 'test.gds.tmp'
rename 'test.gds.tmp' (5.2K, reduced: 12B)
# of fragments: 4
FUNCTION: digest.gdsn
+ raw1 { Int8 131072, 128.0K } *< md5: d9f2acbc0e4257888758ff6ece5f8411; md5_r: d9f2acbc0e4257888758ff6ece5f8411; sha1: daf4efc3cf7278062825d7e4798142baf8ab4aba; sha256: a5b212f05fa19517c71de0853b69f984e4cc50bc4457d1ad7a78d21a8d313fe6; sha512: a55d41e3a09355ad937014a58269d90fdf2a609944ef3b3d9d2033add3a4d8b108d573c1a541fb6c06e1d53d35a6a24180fb2abe6df3e9238fdd9397e8c5edb1
+ raw1 { Int8 131072, 128.0K }
FUNCTION: gds.class
FUNCTION: gdsfmt-package
[1] 1 2 3 4 5 6 7 8 9 10
[1] 11 12 13 14 15 16 17 18 19 20
[1] 21 22 23 24 25 26 27 28 29 30
[1] 31 32 33 34 35 36 37 38 39 40
[1] 41 42 43 44 45 46 47 48 49 50
[1] 51 52 53 54 55 56 57 58 59 60
[1] 1 3 5 7 9
[1] 21 23 25 27 29
[1] 41 43 45 47 49
FUNCTION: gdsn.class
FUNCTION: get.attr.gdsn
FUNCTION: getfile.gdsn
FUNCTION: getfolder.gdsn
FUNCTION: index.gdsn
FUNCTION: is.element.gdsn
FUNCTION: lasterr.gds
FUNCTION: ls.gdsn
FUNCTION: moveto.gdsn
FUNCTION: name.gdsn
FUNCTION: objdesp.gdsn
FUNCTION: openfn.gds
FUNCTION: permdim.gdsn
Clean up the fragments of GDS file:
open the file 'test.gds' (1.1K)
# of fragments: 8
save to 'test.gds.tmp'
rename 'test.gds.tmp' (726B, reduced: 351B)
# of fragments: 5
FUNCTION: print.gds.class
File: /Users/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds (224B)
+ [ ]
|--+ int { Int32 100, 400B }
\--+ int.matrix { Int32 100x50, 19.5K } *
File: /Users/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds (20.3K)
+ [ ]
|--+ int { Int32 100, 400B }
\--+ int.matrix { Int32 100x50, 19.5K } *< int: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
File: /Users/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds (20.3K)
+ [ ]
|--+ int { Int32 100, 400B }
\--+ int.matrix { Int32 100x50, 19.5K } *< int: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
+ int { Int32 100, 400B }
Preview:
1
2
3
4
5
6
...
95
96
97
98
99
100
+ int.matrix { Int32 100x50, 19.5K } *< int: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
Preview:
1 101 201 301 401 501 .. 4401 4501 4601 4701 4801 4901
2 102 202 302 402 502 .. 4402 4502 4602 4702 4802 4902
3 103 203 303 403 503 .. 4403 4503 4603 4703 4803 4903
4 104 204 304 404 504 .. 4404 4504 4604 4704 4804 4904
5 105 205 305 405 505 .. 4405 4505 4605 4705 4805 4905
6 106 206 306 406 506 .. 4406 4506 4606 4706 4806 4906
......
95 195 295 395 495 595 .. 4495 4595 4695 4795 4895 4995
96 196 296 396 496 596 .. 4496 4596 4696 4796 4896 4996
97 197 297 397 497 597 .. 4497 4597 4697 4797 4897 4997
98 198 298 398 498 598 .. 4498 4598 4698 4798 4898 4998
99 199 299 399 499 599 .. 4499 4599 4699 4799 4899 4999
100 200 300 400 500 600 .. 4500 4600 4700 4800 4900 5000
FUNCTION: put.attr.gdsn
FUNCTION: read.gdsn
FUNCTION: readex.gdsn
FUNCTION: readmode.gdsn
FUNCTION: rename.gdsn
FUNCTION: setdim.gdsn
FUNCTION: showfile.gds
FileName ReadOnly
1 /Users/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds FALSE
State
1 open
FileName ReadOnly
1 /Users/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds FALSE
State
1 closed
FUNCTION: summarize.gdsn
FUNCTION: sync.gds
FUNCTION: system.gds
FUNCTION: write.gdsn
RUNIT TEST PROTOCOL -- Wed Oct 16 03:03:52 2019
***********************************************
Number of test functions: 25
Number of errors: 0
Number of failures: 0
1 Test Suite :
gdsfmt RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
160.249 35.498 199.182
gdsfmt.Rcheck/gdsfmt-Ex.timings
| name | user | system | elapsed | |
| add.gdsn | 0.126 | 0.022 | 0.149 | |
| addfile.gdsn | 0.009 | 0.005 | 0.014 | |
| addfolder.gdsn | 0.035 | 0.008 | 0.042 | |
| append.gdsn | 0.015 | 0.004 | 0.018 | |
| apply.gdsn | 0.057 | 0.025 | 0.082 | |
| assign.gdsn | 0.031 | 0.014 | 0.045 | |
| cache.gdsn | 0.003 | 0.001 | 0.004 | |
| cleanup.gds | 0.015 | 0.005 | 0.020 | |
| closefn.gds | 0.001 | 0.001 | 0.003 | |
| clusterApply.gdsn | 0.073 | 0.033 | 1.381 | |
| cnt.gdsn | 0.002 | 0.003 | 0.004 | |
| compression.gdsn | 0.005 | 0.003 | 0.008 | |
| copyto.gdsn | 0.035 | 0.005 | 0.040 | |
| createfn.gds | 0.006 | 0.002 | 0.007 | |
| delete.attr.gdsn | 0.005 | 0.002 | 0.007 | |
| delete.gdsn | 0.014 | 0.002 | 0.017 | |
| diagnosis.gds | 0.025 | 0.007 | 0.032 | |
| digest.gdsn | 0.076 | 0.017 | 0.093 | |
| gdsfmt-package | 0.043 | 0.010 | 0.054 | |
| get.attr.gdsn | 0.004 | 0.003 | 0.007 | |
| getfile.gdsn | 0.013 | 0.005 | 0.018 | |
| getfolder.gdsn | 0.032 | 0.004 | 0.036 | |
| index.gdsn | 0.014 | 0.002 | 0.017 | |
| is.element.gdsn | 0.004 | 0.004 | 0.008 | |
| lasterr.gds | 0.000 | 0.001 | 0.001 | |
| ls.gdsn | 0.003 | 0.003 | 0.006 | |
| moveto.gdsn | 0.045 | 0.006 | 0.051 | |
| name.gdsn | 0.002 | 0.001 | 0.003 | |
| objdesp.gdsn | 0.013 | 0.005 | 0.018 | |
| openfn.gds | 0.007 | 0.003 | 0.010 | |
| permdim.gdsn | 0.015 | 0.007 | 0.021 | |
| print.gds.class | 0.018 | 0.003 | 0.021 | |
| put.attr.gdsn | 0.007 | 0.004 | 0.009 | |
| read.gdsn | 0.020 | 0.006 | 0.026 | |
| readex.gdsn | 0.012 | 0.007 | 0.019 | |
| readmode.gdsn | 0.004 | 0.002 | 0.007 | |
| rename.gdsn | 0.012 | 0.002 | 0.013 | |
| setdim.gdsn | 0.013 | 0.005 | 0.021 | |
| showfile.gds | 0.008 | 0.002 | 0.010 | |
| summarize.gdsn | 0.004 | 0.003 | 0.008 | |
| sync.gds | 0.004 | 0.002 | 0.006 | |
| system.gds | 0.013 | 0.004 | 0.016 | |
| write.gdsn | 0.003 | 0.003 | 0.006 | |