H5Zblosc.c:51:10: fatal error: 'H5PLextern.h' file not found

Question

H5Zblosc.c:51:10: fatal error: 'H5PLextern.h' file not found

colinbrislawn opened this issue 3 years ago · 6 comments

I'm installing this package on an M1 mac and I'm getting this error. Any idea?

arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -c -o H5Zblosc.o H5Zblosc.c \
"-DHAVE_WORKING_LOG1P" -I./lib/blosc-1.20.1
H5Zblosc.c:51:10: fatal error: 'H5PLextern.h' file not found
#include <H5PLextern.h>
         ^~~~~~~~~~~~~~
1 error generated.

Full command and error:

> BiocManager::install("rhdf5filters")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'rhdf5filters'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/rhdf5filters_1.6.0.tar.gz'
Content type 'application/x-gzip' length 854552 bytes (834 KB)
==================================================
downloaded 834 KB

* installing *source* package ‘rhdf5filters’ ...
** using staged installation
configuring the BLOSC filter...
x86_CPU=false
checking for arm64-apple-darwin20.0.0-gcc... arm64-apple-darwin20.0.0-clang
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 we are using the GNU C compiler... yes
checking whether arm64-apple-darwin20.0.0-clang accepts -g... yes
checking for arm64-apple-darwin20.0.0-clang option to accept ISO C89... none needed
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -mavx2... yes
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
configure:    BZIP2_LIB=bzip2/libH5Zbz2.so
configure:    BLOSC_LIB=blosc/libH5Zblosc.so
configure:    LZF_LIB=lzf/libH5Zlzf.so
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/Makevars
** libs
make -C blosc
make[1]: Entering directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/snappy-1.1.1'
arm64-apple-darwin20.0.0-clang++ -std=gnu++14 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -c snappy.cc
arm64-apple-darwin20.0.0-clang++ -std=gnu++14 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -c snappy-c.cc
arm64-apple-darwin20.0.0-clang++ -std=gnu++14 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -c snappy-sinksource.cc
arm64-apple-darwin20.0.0-clang++ -std=gnu++14 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.2
make[2]: Entering directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/lz4-1.9.2'
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -c lz4.c
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -c lz4hc.c
make[2]: Leaving directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/lz4-1.9.2'
make -C lib/zstd-1.4.5
make[2]: Entering directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/zstd-1.4.5'
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/zstd-1.4.5'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/blosc-1.20.1'
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c bitshuffle-generic.c
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c shuffle-generic.c
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5     -c shuffle.c
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosclz.c
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosc.c
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC "-DHAVE_WORKING_LOG1P" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c fastcopy.c
make[2]: Leaving directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
arm64-apple-darwin20.0.0-ar cq libblosc.a lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o
arm64-apple-darwin20.0.0-ranlib libblosc.a
arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/cbrisl/miniforge3/envs/phyloseq/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1638516560816/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/Users/cbrisl/miniforge3/envs/phyloseq=/usr/local/src/conda-prefix -fPIC -c -o H5Zblosc.o H5Zblosc.c \
"-DHAVE_WORKING_LOG1P" -I./lib/blosc-1.20.1
H5Zblosc.c:51:10: fatal error: 'H5PLextern.h' file not found
#include <H5PLextern.h>
         ^~~~~~~~~~~~~~
1 error generated.
make[1]: *** [Makefile:34: H5Zblosc.o] Error 1
make[1]: Leaving directory '/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/RtmpTMfr28/R.INSTALL12d29792894cf/rhdf5filters/src/blosc'
make: *** [Makevars:30: blosc/libH5Zblosc.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/Users/cbrisl/miniforge3/envs/phyloseq/lib/R/library/rhdf5filters’

The downloaded source packages are in
	‘/private/var/folders/8_/0ps3d2mn1cq_j0mkjj80br2r0000gn/T/Rtmp7WxcRs/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'ape', 'backports', 'broom', 'carData', 'class', 'cli', 'DBI', 'fansi', 'foreign', 'glue', 'igraph', 'jsonlite', 'knitr', 'later', 'magrittr', 'MASS', 'Matrix',
  'nlme', 'nnet', 'parallelly', 'pillar', 'progressr', 'Rcpp', 'rlang', 'rpart', 'testthat', 'tinytex', 'xfun', 'yaml'
Update all/some/none? [a/s/n]: 
n
Warning message:
In .inet_warning(msg) :
  installation of package ‘rhdf5filters’ had non-zero exit status

Answer 1 · 2022-01-28T08:10:13.000Z

This is missing a link instruction to the Rhdf5lib package which provides that header.

On the bioconductor builder you can see:

-I"/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include"

I don't know why that statement is missing, because Rhdf5lib should be a prerequisite for rhdf5filters, but I suspect it's because you're using R via conda.

Generally, if I'm using conda, I find it's better to let conda also install packages directly rather than using BiocManager::install() e.g. from https://anaconda.org/bioconda/bioconductor-rhdf5filters

Answer 2 · 2022-01-28T14:17:29.000Z

I don't know why that statement is missing, because Rhdf5lib should be a prerequisite for rhdf5filters, but I suspect it's because you're using R via conda.

Ah! When I went to install Rhdf5lib, the package manager tried to install rhdf5filters first, so I wonder if there is a circular dependency here.

I really like your idea of using conda to install this package. For now, only conda-forge provides builds on the osx-arm64 platform, so I'm relient on a -c conda-forge package or a native build. I know this is a big ask, but is there any chance of moving this build from bioconda to conda-forge, which would provide Windows and also osx-arm64 support?

Answer 3 · 2022-02-01T10:12:20.000Z

Ah! When I went to install Rhdf5lib, the package manager tried to install rhdf5filters first, so I wonder if there is a circular dependency here.

Are you sure about this? There's three related packages that I maintain: Rhdf5lib, rhdf5filters, rhdf5 and the dependency chain should be in that order. I don't use bioconda much, so it might be there's some settings that are different from my usual experience, but Rhdf5lib should be free of any dependencies. I'm surprised that you can even try to install rhdf5filters without it being present, but maybe my configure script can print something more informative if those headers are not found.

I really like your idea of using conda to install this package. For now, only conda-forge provides builds on the osx-arm64 platform, so I'm relient on a -c conda-forge package or a native build. I know this is a big ask, but is there any chance of moving this build from bioconda to conda-forge, which would provide Windows and also osx-arm64 support?

I don't actually have any influence over the presence of the package in bioconda or any of the other conda repositories. The bioconda team have their own pipelines for packaging all the Bioconductor package en masse.

Answer 4 · 2022-02-01T15:01:40.000Z

Thank you for helping me sort this out!

I made a mistake; Rhdf5lib was built just fine using BiocManager. I got the error when trying to install rhdf5filters, so the dependencies are working as you described. However, that same error appears when building rhdf5filters with BiocManager.

CRAN: > package ‘rhdf5filters’ is not available for this version of R
Conda: > PackagesNotFoundError: The following packages are not available from current channels:

r-rhdf5filters

Current channels:

So... anyone can build and submit a conda-forge feedstock, adding their package to conda-forge. But that's only if you want to support a 3rd build platform, in addition to CRAN and BiocManager. 😜

For now, how do I manually patch my BiocManager build to add that missing include:
-I"/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include"

Answer 5 · 2022-02-02T13:34:21.000Z

What do you get if you run this command in an R session?:

system.file("include", package="Rhdf5lib")

The path returned by that is the directory you'll need to include. I expect you could force it to be included in the search path by adding that path to $HOME/.R/Makevars. Something like:

CPPFLAGS=-I"/path/to/Rhdf5lib/include"

However it's a bit concerning that it doesn't find it automatically during installation. That means one of my installation assumptions is wrong for your setup.

Answer 6 · 2022-02-02T14:49:02.000Z

It worked!

> system.file("include", package="Rhdf5lib")
[1] "/Users/cbrisl/miniforge3/envs/phyloseq/lib/R/library/Rhdf5lib/include"

>$ grep CPP ~/.R/Makevars
PKG_CPPFLAGS=-I"/Users/cbrisl/miniforge3/envs/phyloseq/lib/R/library/Rhdf5lib/include"
export PKG_CPPFLAGS

Thank you so much for you help!

Feel free to close this issue, or

That means one of my installation assumptions is wrong for your setup.

could I help you troubleshoot this for the other M1 apple silicon folks out there?