I just installed new Ubuntu updates, and apparently it contained a new version of R (4.3.0), which I didn't realize. I ended up having to reinstall some packages, but there is one that I am having issues, which is 'Phyloseq'. This is the error message I get:
blosc.c:37:12: fatal error: zstd.h: No such file or directory
37 | #include "zstd.h"
| ^~~~~~~~
compilation terminated.
I tried installing Phyloseq from the terminal as root, but it didn't work either. Also, I checked whether zstd is installed, and it's there (v1.4.4). Any ideas how to solve it? I'm using Ubuntu 20.04.
Many thanks in advance!
This is the full output of the installation command
BiocManager::install("phyloseq")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'phyloseq'
also installing the dependencies ‘rhdf5filters’, ‘rhdf5’, ‘biomformat’
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5filters_1.12.0.tar.gz'
Content type 'application/x-gzip' length 2959706 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5_2.44.0.tar.gz'
Content type 'application/x-gzip' length 1249545 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/biomformat_1.28.0.tar.gz'
Content type 'application/x-gzip' length 301144 bytes (294 KB)
==================================================
downloaded 294 KB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/phyloseq_1.44.0.tar.gz'
Content type 'application/x-gzip' length 5689663 bytes (5.4 MB)
==================================================
downloaded 5.4 MB
* installing *source* package ‘rhdf5filters’ ...
** using staged installation
configuring the BLOSC filter...
x86_CPU=true
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
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: 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: VBZ_LIB=vbz/libH5Zvbz.so
configure: ZSTD_LIB=zstd/libH5Zzstd.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
using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
make -C zstd
make[1]: Entering directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/zstd'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
rm -f libzstd.a
ar cq libzstd.a common/debug.o common/entropy_common.o common/error_private.o common/fse_decompress.o common/pool.o common/threading.o common/xxhash.o common/zstd_common.o compress/fse_compress.o compress/hist.o compress/huf_compress.o compress/zstd_compress.o compress/zstd_compress_literals.o compress/zstd_compress_sequences.o compress/zstd_compress_superblock.o compress/zstd_double_fast.o compress/zstd_fast.o compress/zstd_lazy.o compress/zstd_ldm.o compress/zstd_opt.o compress/zstdmt_compress.o decompress/huf_decompress.o decompress/zstd_ddict.o decompress/zstd_decompress.o decompress/zstd_decompress_block.o
ranlib libzstd.a
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared H5Zzstd.c -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" \
libzstd.a -Wl,-Bsymbolic-functions -Wl,-z,relro -o libH5Zzstd.so
make[1]: Leaving directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc/lib/lz4-1.9.4'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lz4.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lz4hc.c
make[2]: Leaving directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc/lib/lz4-1.9.4'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-avx2.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-avx2.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-sse2.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-sse2.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-generic.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-generic.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosclz.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/meb/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosc.c
blosc.c:37:12: fatal error: zstd.h: No such file or directory
37 | #include "zstd.h"
| ^~~~~~~~
compilation terminated.
make[2]: Leaving directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc/lib/blosc-1.20.1'
make[2]: *** [Makefile:28: blosc.o] Error 1
make[1]: *** [Makefile:39: blosc] Error 2
make[1]: Leaving directory '/tmp/Rtmpc8Fxc6/R.INSTALL2b49235ec4b9/rhdf5filters/src/blosc'
make: *** [Makevars:37: libH5Zblosc.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/home/meb/R/x86_64-pc-linux-gnu-library/4.3/rhdf5filters’
ERROR: dependency ‘rhdf5filters’ is not available for package ‘rhdf5’
* removing ‘/home/meb/R/x86_64-pc-linux-gnu-library/4.3/rhdf5’
ERROR: dependency ‘rhdf5’ is not available for package ‘biomformat’
* removing ‘/home/meb/R/x86_64-pc-linux-gnu-library/4.3/biomformat’
ERROR: dependency ‘biomformat’ is not available for package ‘phyloseq’
* removing ‘/home/meb/R/x86_64-pc-linux-gnu-library/4.3/phyloseq’
The downloaded source packages are in
‘/tmp/RtmptEU44k/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, foreign, lattice, MASS, Matrix, spatial
Warning messages:
1: In install.packages(...) :
installation of package ‘rhdf5filters’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘rhdf5’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘biomformat’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘phyloseq’ had non-zero exit status
