r-hdf5array fails to build

DoneSubmitted by Björn Höfling.
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2 participants
  • Björn Höfling
  • zimoun
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normal
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Björn Höfling wrote on 17 Jul 2020 12:14
(address . bug-guix@gnu.org)
20200717121414.056f6ddf@alma-ubu
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** libsgcc -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.ogcc -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.ogcc -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.ogcc -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.ogcc -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.ogcc -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.ogcc -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 -lRgcc: error: /gnu/store/cfr4bbglibavxbqxhn3pg3pfar6qqpiw-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libsz.a: No such file or directorymake: *** [/gnu/store/yd83ibzxjrb7cgcc6d4smx4pqcdl8r3p-r-minimal-4.0.2/lib/R/share/make/shlib.mk:6: HDF5Array.so] Error 1ERROR: 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 1note: 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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zimoun wrote on 28 Oct 2020 20:13
(name . Björn Höfling)(address . bjoern.hoefling@bjoernhoefling.de)(address . 42405@debbugs.gnu.org)
86lffqyxhl.fsf@gmail.com
Dear,
On Fri, 17 Jul 2020 at 12:14, Björn Höfling <bjoern.hoefling@bjoernhoefling.de> wrote:
Toggle quote (2 lines)> It is missing the (proprietary) SZIP Compression Library.
Well, it built fine with 63b75c01c2374edc38437215278f50b617a12c08. Andnow using Guix 02c3c51, I get also fine:
Toggle snippet (41 lines)$ guix build r-hdf5array/gnu/store/qrxrky9jj0mv96yy1875qfwwig7mgsyd-r-hdf5array-1.16.1
$ guix build r-hdf5array --no-grafts --check The following derivation will be built: /gnu/store/l59g16jyb2n2nw2n72qzxa5yapkwai51-r-hdf5array-1.16.1.drvbuilding /gnu/store/l59g16jyb2n2nw2n72qzxa5yapkwai51-r-hdf5array-1.16.1.drv...
[...]
starting phase `install'* installing *source* package ‘HDF5Array’ ...** using staged installation** libsgcc -I"/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/include" -DNDEBUG -I'/gnu/store/c1pkb6xv0zjapcgvjl7ihng65c2q83rw-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5DSetDescriptor.c -o H5DSetDescriptor.ogcc -I"/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/include" -DNDEBUG -I'/gnu/store/c1pkb6xv0zjapcgvjl7ihng65c2q83rw-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-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.ogcc -I"/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/include" -DNDEBUG -I'/gnu/store/c1pkb6xv0zjapcgvjl7ihng65c2q83rw-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.ogcc -I"/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/include" -DNDEBUG -I'/gnu/store/c1pkb6xv0zjapcgvjl7ihng65c2q83rw-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c array_selection.c -o array_selection.ogcc -I"/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/include" -DNDEBUG -I'/gnu/store/c1pkb6xv0zjapcgvjl7ihng65c2q83rw-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5dimscales.c -o h5dimscales.ogcc -I"/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/include" -DNDEBUG -I'/gnu/store/c1pkb6xv0zjapcgvjl7ihng65c2q83rw-r-s4vectors-0.26.1/site-library/S4Vectors/include' -I'/gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5mread.c -o h5mread.ogcc -shared -L/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/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/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libhdf5_hl.a /gnu/store/l95pry5yf7x634jchpvasrsqqqvlx7dm-r-rhdf5lib-1.10.1/site-library/Rhdf5lib/lib/libhdf5.a -lz -L/gnu/store/01xi3sig314wgwa1j9sxk37vl816mj74-r-minimal-4.0.3/lib/R/lib -lRinstalling to /gnu/store/w29frb8jpz0w8xkj7p4rxvs7agzqfpvv-r-hdf5array-1.16.1/site-library/00LOCK-HDF5Array/00new/HDF5Array/libs** R** inst** tests** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (HDF5Array)
[...]
successfully built /gnu/store/l59g16jyb2n2nw2n72qzxa5yapkwai51-r-hdf5array-1.16.1.drv/gnu/store/w29frb8jpz0w8xkj7p4rxvs7agzqfpvv-r-hdf5array-1.16.1
Could you confirm it works for you? If yes, feel free to close the bug?

All the best,simon
Z
Z
zimoun wrote on 20 Dec 2020 08:55
(name . Björn Höfling)(address . bjoern.hoefling@bjoernhoefling.de)(address . 42405@debbugs.gnu.org)
86wnxcrjxf.fsf@gmail.com
Hi,
Toggle quote (10 lines)>> It is missing the (proprietary) SZIP Compression Library.>> Well, it built fine with 63b75c01c2374edc38437215278f50b617a12c08. And> now using Guix 02c3c51, I get also fine:>> $ guix build r-hdf5array> /gnu/store/qrxrky9jj0mv96yy1875qfwwig7mgsyd-r-hdf5array-1.16.1>> $ guix build r-hdf5array --no-grafts --check
[...]
Toggle quote (4 lines)> /gnu/store/w29frb8jpz0w8xkj7p4rxvs7agzqfpvv-r-hdf5array-1.16.1>> Could you confirm it works for you? If yes, feel free to close the bug?
Since it works also with 69b9826 (2020-12-19), substitute available andreproducible build, I am closing.
All the best,simon
Z
Z
zimoun wrote on 20 Dec 2020 08:55
control message for bug #42405
(address . control@debbugs.gnu.org)
86v9cwrjwv.fsf@gmail.com
tags 42405 fixedclose 42405 quit
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