r-hdf5array fails to build

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  • Björn Höfling
  • zimoun
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Björn Höfling
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B
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
** 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
-----BEGIN PGP SIGNATURE-----

iF0EAREKAB0WIQQiGUP0np8nb5SZM4K/KGy2WT5f/QUCXxF59gAKCRC/KGy2WT5f
/RjTAJ4mO5q7txHOP4gSXqc6F8GkmGyhQgCeJyr897tNpvroNbZ17sN5LdRkvbw=
=hgHd
-----END PGP SIGNATURE-----


Z
Z
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. And
now 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.drv
building /gnu/store/l59g16jyb2n2nw2n72qzxa5yapkwai51-r-hdf5array-1.16.1.drv...

[...]

starting phase `install'
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -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.o
gcc -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.o
gcc -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.o
gcc -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.o
gcc -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.o
gcc -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.o
gcc -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 -lR
installing 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 and
reproducible 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 fixed
close 42405
quit
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