GNU bug report logs -
#42405
r-hdf5array fails to build
Previous Next
To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 42405 in the body.
You can then email your comments to 42405 AT debbugs.gnu.org in the normal way.
Toggle the display of automated, internal messages from the tracker.
Report forwarded
to
bug-guix <at> gnu.org
:
bug#42405
; Package
guix
.
(Fri, 17 Jul 2020 10:15:01 GMT)
Full text and
rfc822 format available.
Acknowledgement sent
to
Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de>
:
New bug report received and forwarded. Copy sent to
bug-guix <at> gnu.org
.
(Fri, 17 Jul 2020 10:15:01 GMT)
Full text and
rfc822 format available.
Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
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
[Message part 2 (application/pgp-signature, inline)]
Information forwarded
to
bug-guix <at> gnu.org
:
bug#42405
; Package
guix
.
(Wed, 28 Oct 2020 19:15:02 GMT)
Full text and
rfc822 format available.
Message #8 received at 42405 <at> debbugs.gnu.org (full text, mbox):
Dear,
On Fri, 17 Jul 2020 at 12:14, Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de> wrote:
> It is missing the (proprietary) SZIP Compression Library.
Well, it built fine with 63b75c01c2374edc38437215278f50b617a12c08. And
now using Guix 02c3c51, I get also fine:
--8<---------------cut here---------------start------------->8---
$ 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
--8<---------------cut here---------------end--------------->8---
Could you confirm it works for you? If yes, feel free to close the bug?
All the best,
simon
Information forwarded
to
bug-guix <at> gnu.org
:
bug#42405
; Package
guix
.
(Sun, 20 Dec 2020 07:59:01 GMT)
Full text and
rfc822 format available.
Message #11 received at 42405 <at> debbugs.gnu.org (full text, mbox):
Hi,
>> 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
[...]
> /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
Added tag(s) fixed.
Request was from
zimoun <zimon.toutoune <at> gmail.com>
to
control <at> debbugs.gnu.org
.
(Sun, 20 Dec 2020 07:59:02 GMT)
Full text and
rfc822 format available.
bug closed, send any further explanations to
42405 <at> debbugs.gnu.org and Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de>
Request was from
zimoun <zimon.toutoune <at> gmail.com>
to
control <at> debbugs.gnu.org
.
(Sun, 20 Dec 2020 07:59:02 GMT)
Full text and
rfc822 format available.
bug archived.
Request was from
Debbugs Internal Request <help-debbugs <at> gnu.org>
to
internal_control <at> debbugs.gnu.org
.
(Sun, 17 Jan 2021 12:24:04 GMT)
Full text and
rfc822 format available.
This bug report was last modified 3 years and 100 days ago.
Previous Next
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.