GNU bug report logs - #42405
r-hdf5array fails to build

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From: Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de>
To: 42405 <at> debbugs.gnu.org
Subject: bug#42405: r-hdf5array fails to build
Date: Fri, 17 Jul 2020 12:14:14 +0200

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It is missing the (proprietary) SZIP Compression Library.

Björn


building /gnu/store/awjf253pcjsf8wkl6cigxxd0dxqp97q7-r-hdf5array-1.16.1.drv...
[...]

starting phase `install'
* installing *source* package ?HDF5Array? ...
** using staged installation
** libs
gcc -I"/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/include" -DNDEBUG  -I'/gnu/store/8yrjj7wdbz6x9pnxhmf2ka4fl72yy154-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -I"/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/include" -DNDEBUG  -I'/gnu/store/8yrjj7wdbz6x9pnxhmf2ka4fl72yy154-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -I"/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/include" -DNDEBUG  -I'/gnu/store/8yrjj7wdbz6x9pnxhmf2ka4fl72yy154-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/include" -DNDEBUG  -I'/gnu/store/8yrjj7wdbz6x9pnxhmf2ka4fl72yy154-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c array_selection.c -o array_selection.o
gcc -I"/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/include" -DNDEBUG  -I'/gnu/store/8yrjj7wdbz6x9pnxhmf2ka4fl72yy154-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c h5dimscales.c -o h5dimscales.o
gcc -I"/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/include" -DNDEBUG  -I'/gnu/store/8yrjj7wdbz6x9pnxhmf2ka4fl72yy154-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c h5mread.c -o h5mread.o
gcc -shared -L/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/lib -L/usr/local/lib -o HDF5Array.so H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5dimscales.o h5mread.o /gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libhdf5_hl.a /gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libhdf5.a /gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libsz.a -lz -L/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/lib -lR
gcc: error: /gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libsz.a: No such file or directory
make: *** [/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/share/make/shlib.mk:6: HDF5Array.so] Error 1
ERROR: compilation failed for package ?HDF5Array?
* removing ?/gnu/store/g4lk6nfyfsfcdaw69dwj96n8z8ygzf79-r-hdf5array-1.16.1/site-library/HDF5Array?
command "R" "CMD" "INSTALL" "--install-tests" "--library=/gnu/store/g4lk6nfyfsfcdaw69dwj96n8z8ygzf79-r-hdf5array-1.16.1/site-library/" "--built-timestamp=1970-01-01" "." failed with status 1
note: keeping build directory `/tmp/guix-build-r-hdf5array-1.16.1.drv-0'
builder for `/gnu/store/awjf253pcjsf8wkl6cigxxd0dxqp97q7-r-hdf5array-1.16.1.drv' failed with exit code 1

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