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This page was generated on 2023-03-23 11:06:16 -0400 (Thu, 23 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4536
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4298
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4290
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for rhdf5filters on palomino3


To the developers/maintainers of the rhdf5filters package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5filters.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1681/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5filters 1.11.1  (landing page)
Mike Smith
Snapshot Date: 2023-03-22 14:00:17 -0400 (Wed, 22 Mar 2023)
git_url: https://git.bioconductor.org/packages/rhdf5filters
git_branch: devel
git_last_commit: 3db3b34
git_last_commit_date: 2023-02-22 08:58:52 -0400 (Wed, 22 Feb 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rhdf5filters
Version: 1.11.1
Command: rm -rf rhdf5filters.buildbin-libdir && mkdir rhdf5filters.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=rhdf5filters.buildbin-libdir rhdf5filters_1.11.1.tar.gz
StartedAt: 2023-03-23 10:30:38 -0400 (Thu, 23 Mar 2023)
EndedAt: 2023-03-23 10:31:35 -0400 (Thu, 23 Mar 2023)
EllapsedTime: 57.3 seconds
RetCode: 0
Status:   OK  
PackageFile: rhdf5filters_1.11.1.zip
PackageFileSize: 1.099 MiB

Command output

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###
### Running command:
###
###   rm -rf rhdf5filters.buildbin-libdir && mkdir rhdf5filters.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=rhdf5filters.buildbin-libdir rhdf5filters_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'rhdf5filters' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

using C compiler: 'gcc.exe (GCC) 12.2.0'
`R CMD config MAKE` -C blosc
make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc'
`R CMD config MAKE` -C lib/snappy-1.1.1
make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++17    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/snappy-1.1.1'
`R CMD config MAKE` -C lib/lz4-1.9.2
make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/lz4-1.9.2'
gcc    -c lz4.c
gcc    -c lz4hc.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/lz4-1.9.2'
`R CMD config MAKE` -C lib/zstd-1.4.5
make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/zstd-1.4.5'
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/zstd-1.4.5'
`R CMD config MAKE` -C lib/blosc-1.20.1 all
make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -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]
   40 | }
      | ^
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]
   48 | }
      | ^
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]
   85 | }
      | ^
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]
  109 | }
      | ^
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]
  121 | }
      | ^
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]
  139 | }
      | ^
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]
  204 | }
      | ^
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]
  220 | }
      | ^
gcc    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -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]
   17 | }
      | ^
shuffle-generic.c: In function 'blosc_internal_unshuffle_generic':
shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   25 | }
      | ^
gcc    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5     -c shuffle.c
shuffle.c: In function 'blosc_internal_shuffle':
shuffle.c:390:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  390 | }
      | ^
shuffle.c: In function 'blosc_internal_unshuffle':
shuffle.c:403:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  403 | }
      | ^
shuffle.c: In function 'blosc_internal_bitshuffle':
shuffle.c:430:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  430 | }
      | ^
shuffle.c: In function 'blosc_internal_bitunshuffle':
shuffle.c:457:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  457 | }
      | ^
gcc    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosclz.c
gcc    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosc.c
gcc    -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c fastcopy.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/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/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o
ranlib libblosc.a
gcc    -c -o H5Zblosc.o H5Zblosc.c \
-lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.20.1
g++ -std=gnu++17     -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a -lz
make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/blosc'
`R CMD config MAKE` -C bzip2
make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/bzip2'
`R CMD config MAKE` -C bzip2-1.0.8
make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc    -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc    -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc    -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc    -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc    -D_FILE_OFFSET_BITS=64 -c compress.c
gcc    -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc    -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc    -shared H5Zbzip2.c -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a  -o libH5Zbz2.so
make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/bzip2'
`R CMD config MAKE` -C lzf
make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/lzf'
`R CMD config MAKE` -C lzf
make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/lzf/lzf'
gcc    -c lzf_c.c
gcc    -c lzf_d.c
rm -f liblzf.a
ar cq liblzf.a lzf_c.o lzf_d.o
make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/lzf/lzf'
gcc    -shared H5Zlzf.c -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a  -o libH5Zlzf.so
make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/tmpdir/RtmpULA9j1/R.INSTALL100d478ad3e3f/rhdf5filters/src/lzf'
mkdir -p "F:/biocbuild/bbs-3.17-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64/"
cp blosc/libH5Zblosc.so "F:/biocbuild/bbs-3.17-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zblosc.dll"
cp bzip2/libH5Zbz2.so "F:/biocbuild/bbs-3.17-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zbz2.dll"
cp lzf/libH5Zlzf.so "F:/biocbuild/bbs-3.17-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zlzf.dll"
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -s -static-libgcc -o rhdf5filters.dll tmp.def rhdf5filters.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* MD5 sums
packaged installation of 'rhdf5filters' as rhdf5filters_1.11.1.zip
* DONE (rhdf5filters)