Mike Smith
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/rhdf5filters |
| Branch: RELEASE_3_12 |
| Last Commit: 04dcf6e |
| Last Changed Date: 2021-05-03 08:07:27 -0400 (Mon, 03 May 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:15 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the rhdf5filters package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1523/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhdf5filters 1.2.1 (landing page) Mike Smith
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: rhdf5filters |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5filters.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rhdf5filters_1.2.1.tar.gz |
| StartedAt: 2021-05-06 06:12:19 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:12:44 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 24.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rhdf5filters.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5filters.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rhdf5filters_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'rhdf5filters/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rhdf5filters' version '1.2.1' * package encoding: UTF-8 * 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 whether package 'rhdf5filters' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 shell scripts ... 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 ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/rhdf5filters/libs/i386/rhdf5filters.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/rhdf5filters/libs/x64/rhdf5filters.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.Rcheck/00check.log' for details.
rhdf5filters.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/rhdf5filters_1.2.1.tar.gz && rm -rf rhdf5filters.buildbin-libdir && mkdir rhdf5filters.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5filters.buildbin-libdir rhdf5filters_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL rhdf5filters_1.2.1.zip && rm rhdf5filters_1.2.1.tar.gz rhdf5filters_1.2.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'rhdf5filters' ...
** using staged installation
** libs
`R CMD config MAKE` -C blosc
make[1]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc'
`R CMD config MAKE` -C lib/snappy-1.1.1
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/snappy-1.1.1'
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy.cc
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/snappy-1.1.1'
`R CMD config MAKE` -C lib/lz4-1.8.3
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/lz4-1.8.3'
"C:/rtools40/mingw32/bin/"gcc -c lz4.c
"C:/rtools40/mingw32/bin/"gcc -c lz4hc.c
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/lz4-1.8.3'
`R CMD config MAKE` -C lib/zstd-1.3.8
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/zstd-1.3.8'
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
"C:/rtools40/mingw32/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/zstd-1.3.8'
`R CMD config MAKE` -C lib/blosc-1.16.3 all
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/blosc-1.16.3'
"C:/rtools40/mingw32/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c bitshuffle-generic.c
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_remainder':
bitshuffle-generic.c:40:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_scal':
bitshuffle-generic.c:48:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_byte_remainder':
bitshuffle-generic.c:85:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_elem':
bitshuffle-generic.c:109:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bitrow_eight':
bitshuffle-generic.c:121:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_elem_scal':
bitshuffle-generic.c:139:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_scal':
bitshuffle-generic.c:204:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_untrans_bit_elem_scal':
bitshuffle-generic.c:220:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
"C:/rtools40/mingw32/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c shuffle-generic.c
shuffle-generic.c: In function 'blosc_internal_shuffle_generic':
shuffle-generic.c:17:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle-generic.c: In function 'blosc_internal_unshuffle_generic':
shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
"C:/rtools40/mingw32/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c shuffle.c
shuffle.c: In function 'blosc_internal_shuffle':
shuffle.c:382:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle.c: In function 'blosc_internal_unshuffle':
shuffle.c:395:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle.c: In function 'blosc_internal_bitshuffle':
shuffle.c:416:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle.c: In function 'blosc_internal_bitunshuffle':
shuffle.c:437:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
"C:/rtools40/mingw32/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c blosclz.c
"C:/rtools40/mingw32/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c blosc.c
"C:/rtools40/mingw32/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c fastcopy.c
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc/lib/blosc-1.16.3'
rm -f libblosc.a
"C:/rtools40/mingw32/bin/"ar cq libblosc.a lib/blosc-1.16.3/blosc.o lib/blosc-1.16.3/bitshuffle-generic.o lib/blosc-1.16.3/blosclz.o lib/blosc-1.16.3/shuffle.o lib/blosc-1.16.3/fastcopy.o lib/blosc-1.16.3/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.8.3/lz4.o lib/lz4-1.8.3/lz4hc.o lib/zstd-1.3.8/common/debug.o lib/zstd-1.3.8/common/entropy_common.o lib/zstd-1.3.8/common/error_private.o lib/zstd-1.3.8/common/fse_decompress.o lib/zstd-1.3.8/common/pool.o lib/zstd-1.3.8/common/threading.o lib/zstd-1.3.8/common/xxhash.o lib/zstd-1.3.8/common/zstd_common.o lib/zstd-1.3.8/compress/fse_compress.o lib/zstd-1.3.8/compress/hist.o lib/zstd-1.3.8/compress/huf_compress.o lib/zstd-1.3.8/compress/zstd_compress.o lib/zstd-1.3.8/compress/zstd_double_fast.o lib/zstd-1.3.8/compress/zstd_fast.o lib/zstd-1.3.8/compress/zstd_lazy.o lib/zstd-1.3.8/compress/zstd_ldm.o lib/zstd-1.3.8/compress/zstd_opt.o lib/zstd-1.3.8/compress/zstdmt_compress.o lib/zstd-1.3.8/decompress/huf_decompress.o lib/zstd-1.3.8/decompress/zstd_ddict.o lib/zstd-1.3.8/decompress/zstd_decompress.o lib/zstd-1.3.8/decompress/zstd_decompress_block.o
"C:/rtools40/mingw32/bin/"ranlib libblosc.a
"C:/rtools40/mingw32/bin/"gcc -c -o H5Zblosc.o H5Zblosc.c \
-lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.16.3
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a -lz
make[1]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/blosc'
`R CMD config MAKE` -C bzip2
make[1]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/bzip2'
`R CMD config MAKE` -C bzip2-1.0.8
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/bzip2/bzip2-1.0.8'
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c blocksort.c
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c huffman.c
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c crctable.c
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c randtable.c
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c compress.c
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c decompress.c
"C:/rtools40/mingw32/bin/"gcc -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
"C:/rtools40/mingw32/bin/"ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
C:/rtools40/mingw32/bin/ranlib libbz2.a
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/bzip2/bzip2-1.0.8'
"C:/rtools40/mingw32/bin/"gcc -shared H5Zbzip2.c -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -o libH5Zbz2.so
make[1]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpmgRmwQ/R.INSTALL122c54d31f95/rhdf5filters/src/bzip2'
mkdir -p "C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/i386/"
cp blosc/libH5Zblosc.so "C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/i386//libH5Zblosc.dll"
cp bzip2/libH5Zbz2.so "C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/i386//libH5Zbz2.dll"
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhdf5filters.c -o rhdf5filters.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o rhdf5filters.dll tmp.def rhdf5filters.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rhdf5filters'
finding HTML links ... done
hdf5_plugin_path html
rhdf5filters html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'rhdf5filters' ...
** libs
`R CMD config MAKE` -C blosc
make[1]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc'
`R CMD config MAKE` -C lib/snappy-1.1.1
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/snappy-1.1.1'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/snappy-1.1.1'
`R CMD config MAKE` -C lib/lz4-1.8.3
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/lz4-1.8.3'
"C:/rtools40/mingw64/bin/"gcc -c lz4.c
"C:/rtools40/mingw64/bin/"gcc -c lz4hc.c
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/lz4-1.8.3'
`R CMD config MAKE` -C lib/zstd-1.3.8
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/zstd-1.3.8'
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
"C:/rtools40/mingw64/bin/"gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/zstd-1.3.8'
`R CMD config MAKE` -C lib/blosc-1.16.3 all
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/blosc-1.16.3'
"C:/rtools40/mingw64/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c bitshuffle-generic.c
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_remainder':
bitshuffle-generic.c:40:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_scal':
bitshuffle-generic.c:48:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_byte_remainder':
bitshuffle-generic.c:85:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_elem':
bitshuffle-generic.c:109:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bitrow_eight':
bitshuffle-generic.c:121:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_elem_scal':
bitshuffle-generic.c:139:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_scal':
bitshuffle-generic.c:204:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_untrans_bit_elem_scal':
bitshuffle-generic.c:220:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
"C:/rtools40/mingw64/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c shuffle-generic.c
shuffle-generic.c: In function 'blosc_internal_shuffle_generic':
shuffle-generic.c:17:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle-generic.c: In function 'blosc_internal_unshuffle_generic':
shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
"C:/rtools40/mingw64/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c shuffle.c
shuffle.c: In function 'blosc_internal_shuffle':
shuffle.c:382:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle.c: In function 'blosc_internal_unshuffle':
shuffle.c:395:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle.c: In function 'blosc_internal_bitshuffle':
shuffle.c:416:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
shuffle.c: In function 'blosc_internal_bitunshuffle':
shuffle.c:437:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
"C:/rtools40/mingw64/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c blosclz.c
"C:/rtools40/mingw64/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c blosc.c
"C:/rtools40/mingw64/bin/"gcc -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -c fastcopy.c
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc/lib/blosc-1.16.3'
rm -f libblosc.a
"C:/rtools40/mingw64/bin/"ar cq libblosc.a lib/blosc-1.16.3/blosc.o lib/blosc-1.16.3/bitshuffle-generic.o lib/blosc-1.16.3/blosclz.o lib/blosc-1.16.3/shuffle.o lib/blosc-1.16.3/fastcopy.o lib/blosc-1.16.3/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.8.3/lz4.o lib/lz4-1.8.3/lz4hc.o lib/zstd-1.3.8/common/debug.o lib/zstd-1.3.8/common/entropy_common.o lib/zstd-1.3.8/common/error_private.o lib/zstd-1.3.8/common/fse_decompress.o lib/zstd-1.3.8/common/pool.o lib/zstd-1.3.8/common/threading.o lib/zstd-1.3.8/common/xxhash.o lib/zstd-1.3.8/common/zstd_common.o lib/zstd-1.3.8/compress/fse_compress.o lib/zstd-1.3.8/compress/hist.o lib/zstd-1.3.8/compress/huf_compress.o lib/zstd-1.3.8/compress/zstd_compress.o lib/zstd-1.3.8/compress/zstd_double_fast.o lib/zstd-1.3.8/compress/zstd_fast.o lib/zstd-1.3.8/compress/zstd_lazy.o lib/zstd-1.3.8/compress/zstd_ldm.o lib/zstd-1.3.8/compress/zstd_opt.o lib/zstd-1.3.8/compress/zstdmt_compress.o lib/zstd-1.3.8/decompress/huf_decompress.o lib/zstd-1.3.8/decompress/zstd_ddict.o lib/zstd-1.3.8/decompress/zstd_decompress.o lib/zstd-1.3.8/decompress/zstd_decompress_block.o
"C:/rtools40/mingw64/bin/"ranlib libblosc.a
"C:/rtools40/mingw64/bin/"gcc -c -o H5Zblosc.o H5Zblosc.c \
-lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.16.3
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a -lz
make[1]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/blosc'
`R CMD config MAKE` -C bzip2
make[1]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/bzip2'
`R CMD config MAKE` -C bzip2-1.0.8
make[2]: Entering directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/bzip2/bzip2-1.0.8'
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c blocksort.c
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c huffman.c
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c crctable.c
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c randtable.c
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c compress.c
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c decompress.c
"C:/rtools40/mingw64/bin/"gcc -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
"C:/rtools40/mingw64/bin/"ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
C:/rtools40/mingw64/bin/ranlib libbz2.a
make[2]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/bzip2/bzip2-1.0.8'
"C:/rtools40/mingw64/bin/"gcc -shared H5Zbzip2.c -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -o libH5Zbz2.so
make[1]: Leaving directory '/c/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqQ1Nc6/R.INSTALLef827fe5921/rhdf5filters/src/bzip2'
mkdir -p "C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/rhdf5filters/lib/x64/"
cp blosc/libH5Zblosc.so "C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/rhdf5filters/lib/x64//libH5Zblosc.dll"
cp bzip2/libH5Zbz2.so "C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/rhdf5filters/lib/x64//libH5Zbz2.dll"
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -lpthread -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include" -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rhdf5filters.c -o rhdf5filters.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o rhdf5filters.dll tmp.def rhdf5filters.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/rhdf5filters.buildbin-libdir/rhdf5filters/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5filters' as rhdf5filters_1.2.1.zip
* DONE (rhdf5filters)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'rhdf5filters' successfully unpacked and MD5 sums checked
|
rhdf5filters.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> library(testthat)
> library(rhdf5filters)
>
> test_check("rhdf5filters")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
0.98 0.07 1.04
|
rhdf5filters.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> library(testthat)
> library(rhdf5filters)
>
> test_check("rhdf5filters")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
0.96 0.12 1.07
|
|
rhdf5filters.Rcheck/examples_i386/rhdf5filters-Ex.timings
|
rhdf5filters.Rcheck/examples_x64/rhdf5filters-Ex.timings
|