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grimbough / rhdf5filters

Distributing additional HDF5 compression filters as an R package. Intended to be used with rhdf5, however the compiled filters can also be used with external applications.
https://bioconductor.org/packages/rhdf5filters/
BSD 2-Clause "Simplified" License
5 stars 6 forks source link

Compiling error in R-4.3 #20

Closed imerelli closed 11 months ago

imerelli commented 1 year ago

Hi, I have this error while compiling rhdf5filters on R 4.3. Any hint?

make[2]: Entering directory '/home/hpc.tiget/rhdf5filters/src/vbz/vbz'
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/common/tools/ric.tiget/mambaforge/envs/integration/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1682155243464/work=/usr/local/src/conda/r-base-4.3.0 -fdebug-prefix-map=/opt/common/tools/ric.tiget/mambaforge/envs/integration=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/common/tools/ric.tiget/mambaforge/envs/integration/include -I/opt/common/tools/ric.tiget/mambaforge/envs/integration/include -Wl,-rpath-link,/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib -I"/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/R/library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c vbz.cpp -o vbz.o
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/common/tools/ric.tiget/mambaforge/envs/integration/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1682155243464/work=/usr/local/src/conda/r-base-4.3.0 -fdebug-prefix-map=/opt/common/tools/ric.tiget/mambaforge/envs/integration=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/common/tools/ric.tiget/mambaforge/envs/integration/include -I/opt/common/tools/ric.tiget/mambaforge/envs/integration/include -Wl,-rpath-link,/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib -I"/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/R/library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o
In file included from /opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/immintrin.h:37,
                 from /opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/x86intrin.h:32,
                 from v0/vbz_streamvbyte_impl_sse3.h:9,
                 from v0/vbz_streamvbyte_impl.h:92,
                 from v0/vbz_streamvbyte.cpp:2:
/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/tmmintrin.h: In static member function 'static void StreamVByteWorkerV0<short int, true>::compress_int_registers(__m128i, __m128i, char*&, char*&)':
/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:600:30: note: called from here
  600 |         r1 = _mm_shuffle_epi8(r1, r3);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:599:30: note: called from here
  599 |         r0 = _mm_shuffle_epi8(r0, r2);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:600:30: note: called from here
  600 |         r1 = _mm_shuffle_epi8(r1, r3);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/gcc/x86_64-conda-linux-gnu/12.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:599:30: note: called from here
  599 |         r0 = _mm_shuffle_epi8(r0, r2);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
make[2]: *** [Makefile:9: v0/vbz_streamvbyte.o] Error 1
make[2]: Leaving directory '/home/hpc.tiget/rhdf5filters/src/vbz/vbz'
make[1]: *** [Makefile:23: vbz] Error 2
make[1]: Leaving directory '/home/hpc.tiget/rhdf5filters/src/vbz'
make: *** [Makevars:34: libH5Zvbz.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/opt/common/tools/ric.tiget/mambaforge/envs/integration/lib/R/library/rhdf5filters’
ryanhchung commented 1 year ago

I am suffering from the exact same error with the R 4.3 environment. Any solutions?

grimbough commented 1 year ago

I am suffering from the exact same error with the R 4.3 environment. Any solutions?

Are you also using R and/or compilers installed with conda?

Can you include the full output from the package installation here?

prototaxites commented 1 year ago

Also having this issue. Trying to rebuild an {renv} environment that I developed on my laptop. I tried installing the bioconda package bioconductor-rhdf5filters to see if it would fill in any missing dependencies, but no luck.

Conda environment: 

mamba list            
# packages in environment at /groups/jmd20jns/mambaforge/envs/r:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
bioconductor-rhdf5filters 1.12.1            r43hf17093f_1    bioconda
bioconductor-rhdf5lib     1.22.0            r43h217d67c_1    bioconda
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.20.1               hd590300_1    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
cffi                      1.16.0          py312hf06ca03_0    conda-forge
curl                      8.4.0                hca28451_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         13.2.0               h338b0a0_2    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    13.2.0               h76e1118_2    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gxx_impl_linux-64         13.2.0               h338b0a0_2    conda-forge
harfbuzz                  8.2.1                h3d44ed6_0    conda-forge
hdf5                      1.14.2          nompi_h4f84152_100    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_16    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.1.2                h59595ed_1    conda-forge
libblas                   3.9.0           19_linux64_openblas    conda-forge
libboost                  1.82.0               h6fcfa73_6    conda-forge
libboost-devel            1.82.0               h00ab1b0_6    conda-forge
libboost-headers          1.82.0               ha770c72_6    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libdeflate                1.19                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     13.2.0               ha9c7c90_2    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libglib                   2.78.0               hebfc3b9_0    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           19_linux64_openblas    conda-forge
libnghttp2                1.55.1               h47da74e_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsanitizer              13.2.0               h7e041cc_2    conda-forge
libsqlite                 3.44.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  13.2.0               ha9c7c90_2    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libtiff                   4.6.0                ha9c0a0a_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
openssl                   3.1.4                hd590300_0    conda-forge
pango                     1.50.14              ha41ecd1_2    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h59595ed_0    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
python                    3.12.0          hab00c5b_0_cpython    conda-forge
python_abi                3.12                    4_cp312    conda-forge
r-base                    4.3.2                h93585b2_0    conda-forge
radian                    0.6.8              pyhd8ed1ab_0    conda-forge
rchitect                  0.4.4           py312h98912ed_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sysroot_linux-64          2.12                he073ed8_16    conda-forge
tk                        8.6.13               h2797004_0    conda-forge
tktable                   2.10                 h0c5db8f_5    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wcwidth                   0.2.9              pyhd8ed1ab_0    conda-forge
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.7                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxt                1.3.0                hd590300_1    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Install error output below:

> renv::install("bioc::rhdf5filters")

...

Error: Error installing package 'rhdf5filters':
========================================

* installing *source* package ‘rhdf5filters’ ...
** using staged installation
checking for gcc... x86_64-conda-linux-gnu-cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to enable C11 features... none needed
configure: is NOT Bioc build machine
configure: configuring BZIP2 filter...
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for bzlib.h... yes
checking for BZ2_bzDecompressInit in -lbz2... yes
configure: Using system bzip2 library
configure: configuring the Zstd filter...
checking for zstd.h... yes
checking for ZSTD_decompress in -lzstd... yes
configure: Using system Zstd library
configure: configuring the BLOSC filter...
checking for blosc.h... no
configure: compiling bundled BLOSC library
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -mavx2... yes
checking for gcc __builtin_cpu_init function... (cached) true
checking for x86 sse2 instruction support... yes
checking for x86 avx2 instruction support... yes
configure: configuring the VBZ filter
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
configure: creating ./config.status
config.status: creating src/bzip2/Makefile
config.status: creating src/zstd/Makefile
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/vbz/Makefile
config.status: creating src/vbz/third_party/streamvbyte/Makefile
config.status: creating src/Makevars
** libs
using C compiler: ‘x86_64-conda-linux-gnu-cc (conda-forge gcc 13.2.0-2) 13.2.0’
make -C zstd
make[1]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/zstd'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -shared H5Zzstd.c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" \
 -lzstd -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/jmd20jns/mambaforge/envs/r/lib -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -L/groups/jmd20jns/mambaforge/envs/r/lib -o libH5Zzstd.so
make[1]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc/lib/snappy-1.1.1'
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -c snappy.cc
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -c snappy-c.cc
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -c snappy-sinksource.cc
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc/lib/lz4-1.9.4'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -c lz4.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -c lz4hc.c
make[2]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc/lib/lz4-1.9.4'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc/lib/blosc-1.20.1'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-avx2.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-avx2.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-sse2.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-sse2.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-generic.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-generic.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosclz.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosc.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c fastcopy.c
make[2]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
x86_64-conda-linux-gnu-ar cq libblosc.a lib/blosc-1.20.1/bitshuffle-avx2.o lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/shuffle-avx2.o lib/blosc-1.20.1/shuffle-sse2.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/bitshuffle-sse2.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/lz4-1.9.4/lz4.o lib/lz4-1.9.4/lz4hc.o 
x86_64-conda-linux-gnu-ranlib libblosc.a
x86_64-conda-linux-gnu-c++ -std=gnu++17 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -shared -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" H5Zblosc.cpp \
-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/jmd20jns/mambaforge/envs/r/lib -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -L/groups/jmd20jns/mambaforge/envs/r/lib -I./lib/blosc-1.20.1  ./libblosc.a -lzstd -lz -o libH5Zblosc.so 
make[1]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/bzip2'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -shared H5Zbzip2.c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" \
 -lbz2 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/jmd20jns/mambaforge/envs/r/lib -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -L/groups/jmd20jns/mambaforge/envs/r/lib -o libH5Zbz2.so
make[1]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/lzf/lzf'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -c lzf_c.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -c lzf_d.c
rm -f liblzf.a
x86_64-conda-linux-gnu-ar cq liblzf.a lzf_c.o lzf_d.o
x86_64-conda-linux-gnu-ranlib liblzf.a
make[2]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/lzf/lzf'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -shared H5Zlzf.c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/jmd20jns/mambaforge/envs/r/lib -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -L/groups/jmd20jns/mambaforge/envs/r/lib -o libH5Zlzf.so
make[1]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/lzf'
make -C vbz
make[1]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/vbz'
make -C third_party/streamvbyte
make[2]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/vbz/third_party/streamvbyte'
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_decode.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_encode.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbytedelta_decode.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbytedelta_encode.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_0124_encode.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_0124_decode.c
x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_zigzag.c
rm -f libstreamvbyte.a
x86_64-conda-linux-gnu-ar cq libstreamvbyte.a streamvbyte_decode.o streamvbyte_encode.o streamvbytedelta_decode.o streamvbytedelta_encode.o streamvbyte_0124_encode.o  streamvbyte_0124_decode.o streamvbyte_zigzag.o
ranlib libstreamvbyte.a 
make[2]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/vbz/third_party/streamvbyte'
make -C vbz
make[2]: Entering directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/vbz/vbz'
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c vbz.cpp -o vbz.o
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/jmd20jns/mambaforge/envs/r/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/groups/jmd20jns/mambaforge/envs/r=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/jmd20jns/mambaforge/envs/r/include -I/groups/jmd20jns/mambaforge/envs/r/include -Wl,-rpath-link,/groups/jmd20jns/mambaforge/envs/r/lib -I"/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o
In file included from /groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/immintrin.h:37,
                 from /groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/x86intrin.h:32,
                 from v0/vbz_streamvbyte_impl_sse3.h:9,
                 from v0/vbz_streamvbyte_impl.h:93,
                 from v0/vbz_streamvbyte.cpp:2:
/groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h: In static member function 'static void StreamVByteWorkerV0<short int, true>::compress_int_registers(__m128i, __m128i, char*&, char*&)':
/groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:600:30: note: called from here
  600 |         r1 = _mm_shuffle_epi8(r1, r3);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:599:30: note: called from here
  599 |         r0 = _mm_shuffle_epi8(r0, r2);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:600:30: note: called from here
  600 |         r1 = _mm_shuffle_epi8(r1, r3);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/groups/jmd20jns/mambaforge/envs/r/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:599:30: note: called from here
  599 |         r0 = _mm_shuffle_epi8(r0, r2);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
make[2]: *** [Makefile:9: v0/vbz_streamvbyte.o] Error 1
make[2]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/vbz/vbz'
make[1]: *** [Makefile:25: vbz] Error 2
make[1]: Leaving directory '/tmp/Rtmpec7lCf/R.INSTALL11d2ea1e6a4ee0/rhdf5filters/src/vbz'
make: *** [Makevars:29: libH5Zvbz.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/home/people/jmd20jns/test_model/TagJumping/renv/staging/1/rhdf5filters’
install of package 'rhdf5filters' failed [error code 1]
Traceback (most recent calls last):
12: renv::install("bioc::rhdf5filters")
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path)
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)
ryanhchung commented 1 year ago

Hi @grimbough

I am using conda environment, and used BiocManager::install("rhdf5filters").

Also tried to install by conda install -c bioconda bioconductor-rhdf5filters but it takes forever.

Here is my error

make[2]: *** [Makefile:9: v0/vbz_streamvbyte.o] Error 1
make[2]: Leaving directory '/tmp/RtmpTRrny6/R.INSTALL1fc432d2d0eed/rhdf5filters/src/vbz/vbz'
make[1]: *** [Makefile:25: vbz] Error 2
make[1]: Leaving directory '/tmp/RtmpTRrny6/R.INSTALL1fc432d2d0eed/rhdf5filters/src/vbz'
make: *** [Makevars:29: libH5Zvbz.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/home/rchung/miniconda3/envs/r_env/lib/R/library/rhdf5filters’
* restoring previous ‘/home/rchung/miniconda3/envs/r_env/lib/R/library/rhdf5filters’

The downloaded source packages are in
    ‘/tmp/Rtmpk2gYJ5/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
grimbough commented 1 year ago

Thank you everyone for the extra information. Could you try running this command to install a version that hopefully fixes the issue:

BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")
ryanhchung commented 1 year ago

Hi @grimbough , for me still, the same error occurs

Thank you!

QiangShiPKU commented 1 year ago

Thank you everyone for the extra information. Could you try running this command to install a version that hopefully fixes the issue:

BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")

This succeeds for me, but package version installed is 1.13.5 not the newest 1.14.0

dlsoltero commented 1 year ago

Thank you everyone for the extra information. Could you try running this command to install a version that hopefully fixes the issue:

BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")

Hello @grimbough, I tried this also but it didn't worked, I get the same error.

grimbough commented 1 year ago

Thank you everyone for the extra information. Could you try running this command to install a version that hopefully fixes the issue:

BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")

Hello @grimbough, I tried this also but it didn't worked, I get the same error.

Thanks. It be great if you could include a copy of the output so I can try and figure out what compiler settings are wrong. Everything after make[2]: Entering directory '/.../.../rhdf5filters/src/vbz/vbz' would be perfect.

dlsoltero commented 1 year ago

Thanks for the quick reply. Here it is:

make[2]: Entering directory '/tmp/RtmpHPHhHC/R.INSTALL121a07835fdf5/rhdf5filters/src/vbz/vbz'
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/daniel/miniconda3/envs/momix/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/home/daniel/miniconda3/envs/momix=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/daniel/miniconda3/envs/momix/include -I/home/daniel/miniconda3/envs/momix/include -Wl,-rpath-link,/home/daniel/miniconda3/envs/momix/lib -I"/home/daniel/miniconda3/envs/momix/lib/R/library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c vbz.cpp -o vbz.o
x86_64-conda-linux-gnu-c++ -std=gnu++17 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/daniel/miniconda3/envs/momix/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1698915151601/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/home/daniel/miniconda3/envs/momix=/usr/local/src/conda-prefix -fpic -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/daniel/miniconda3/envs/momix/include -I/home/daniel/miniconda3/envs/momix/include -Wl,-rpath-link,/home/daniel/miniconda3/envs/momix/lib -I"/home/daniel/miniconda3/envs/momix/lib/R/library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o
In file included from /home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/immintrin.h:37,
                 from /home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/x86intrin.h:32,
                 from v0/vbz_streamvbyte_impl_sse3.h:9,
                 from v0/vbz_streamvbyte_impl.h:93,
                 from v0/vbz_streamvbyte.cpp:2:
/home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h: In static member function 'static void StreamVByteWorkerV0<short int, true>::compress_int_registers(__m128i, __m128i, char*&, char*&)':
/home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:600:30: note: called from here
  600 |         r1 = _mm_shuffle_epi8(r1, r3);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:599:30: note: called from here
  599 |         r0 = _mm_shuffle_epi8(r0, r2);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:600:30: note: called from here
  600 |         r1 = _mm_shuffle_epi8(r1, r3);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
/home/daniel/miniconda3/envs/momix/lib/gcc/x86_64-conda-linux-gnu/13.2.0/include/tmmintrin.h:136:1: error: inlining failed in call to 'always_inline' '__m128i _mm_shuffle_epi8(__m128i, __m128i)': target specific option mismatch
  136 | _mm_shuffle_epi8 (__m128i __X, __m128i __Y)
      | ^~~~~~~~~~~~~~~~
v0/vbz_streamvbyte_impl_sse3.h:599:30: note: called from here
  599 |         r0 = _mm_shuffle_epi8(r0, r2);
      |              ~~~~~~~~~~~~~~~~^~~~~~~~
make[2]: *** [Makefile:9: v0/vbz_streamvbyte.o] Error 1
make[2]: Leaving directory '/tmp/RtmpHPHhHC/R.INSTALL121a07835fdf5/rhdf5filters/src/vbz/vbz'
make[1]: *** [Makefile:25: vbz] Error 2
make[1]: Leaving directory '/tmp/RtmpHPHhHC/R.INSTALL121a07835fdf5/rhdf5filters/src/vbz'
make: *** [Makevars:29: libH5Zvbz.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
grimbough commented 1 year ago

Thanks @dlsoltero This seems a bit strange, as it looks the changes I made aren't being reflected in your installation. I would now expect the second line in the output you included to end with:

... -I../third_party/ -I../../zstd/ -mssse3 -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o

where the important part is -mssse3. That flag should fix the error, and I thought I had configured the package to either include that or skip this compilation step entirely. It looks like that's not the case on your system, and it's still broken.

If possible, could you try installing again, and somewhere near the start of the output there will be a line saying configuring the VBZ filter. It'd be great to see the next few lines, so I know what the configuration is on your system. For me those lines look like:

configure: configuring the VBZ filter
Using rhdf5filters sse3-conda branch
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
Setting VBZ and STREAMBYTE flags
Substituting real VBZ and STREAMBYTE flags
configure: finished configuring the VBZ filter

For easy reference, the install command is:

BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")
dlsoltero commented 1 year ago

Thanks @dlsoltero This seems a bit strange, as it looks the changes I made aren't being reflected in your installation. I would now expect the second line in the output you included to end with:

... -I../third_party/ -I../../zstd/ -mssse3 -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o

where the important part is -mssse3. That flag should fix the error, and I thought I had configured the package to either include that or skip this compilation step entirely. It looks like that's not the case on your system, and it's still broken.

If possible, could you try installing again, and somewhere near the start of the output there will be a line saying configuring the VBZ filter. It'd be great to see the next few lines, so I know what the configuration is on your system. For me those lines look like:

configure: configuring the VBZ filter
Using rhdf5filters sse3-conda branch
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
Setting VBZ and STREAMBYTE flags
Substituting real VBZ and STREAMBYTE flags
configure: finished configuring the VBZ filter

For easy reference, the install command is:

BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")

Thanks for the help @grimbough, I'm not sure what was the problem but I did a clean install of the whole conda environment and that fixed the issue.