Compiling error in R-4.3
imerelli opened this issue · comments
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’
I am suffering from the exact same error with the R 4.3 environment. Any solutions?
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?
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)
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' ... doneThank 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")Hi @grimbough , for me still, the same error occurs
Thank you!
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
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.
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.
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’
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 filterFor easy reference, the install command is:
BiocManager::install("grimbough/rhdf5filters", ref = "sse3-conda")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.owhere 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 filterFor 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.