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bug#42405: r-hdf5array fails to build
From: |
Björn Höfling |
Subject: |
bug#42405: r-hdf5array fails to build |
Date: |
Fri, 17 Jul 2020 12:14:14 +0200 |
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
pgp_DKJl71XAK.pgp
Description: OpenPGP digital signature
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