Re: [ext] Re: failed to install the python-umap-learn package
Dear Simon, Thank you so much, the build was successful using: guix time-machine --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 \ -C /tmp/chan.scm \ -- package -p .guix-profile -i python-umap-learn best regards, Hong From: zimoun Sent: 30 September 2020 15:54 To: Li, Hong Cc: Ludovic Courtès; help-guix@gnu.org Subject: Re: [ext] Re: failed to install the python-umap-learn package Dear, Please run: echo "%default-channels" > /tmp/chan.scm guix time-machine --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 \ -C /tmp/chan.scm \ -- package -i pyhton-umap-learn This will fix your initial issue, I guess. Exactly, this works in the end. > [h...@max-login3.mdc-berlin.net:~] $ guix time-machine > --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 -C /tmp/chan.scm -- > package -p guix/new/.guix-profile -i python-umap-learn I have not checked in your previous email, but it is the wrong commit. I tried all succeeded commits, and this commit is the first succeeded one from 2020-01-07 03:09:35 https://data.guix.gnu.org/repository/1/branch/master/package/python-umap-learn/output-history > build of > /gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv > failed > View build log at > '/gnu/var/log/guix/drvs/vx/f3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv'. > guix package: error: build of > `/gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv' > failed It could be expected since the package 'python-scikit-learn' is broken: https://data.guix.gnu.org/repository/1/branch/master/package/python-scikit-learn/output-history especially for the commit you are trying (which is not the one you need for the working 'python-umap-learn' package). > Why this commit? 'python-umap-learn' should be broken > > This commit is the most recent succeeded build from 2020-04-18 19:24:20, you > also suggested this commit before. Ah yeah but then what was the previous commit cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523? :-) > [h...@max-login3.mdc-berlin.net:~] $ guix time-machine > --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- help > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... > Updating channel 'guix-bimsb' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb.git'... > Updating channel 'guix-past' from Git repository at > 'https://gitlab.inria.fr/guix-hpc/guix-past'... > Updating channel 'guix-bimsb-nonfree' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb-nonfree.git'... [...] > /builder for > `/gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv' failed > to produce output path > `/gnu/store/9vpcvp00acz4lvglfs1k69a4i05p5hbw-guix-package-cache' > build of /gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv > failed > View build log at > '/gnu/var/log/guix/drvs/ya/j4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv'. > cannot build derivation > `/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv': 1 dependencies > couldn't be built > guix time-machine: error: build of > `/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv' failed This comes from the extra 3 channels you added. If you remove them (see above), then it should work, I guess. Hope that helps, simon
Re: [ext] Re: failed to install the python-umap-learn package
Dear, Please run: echo "%default-channels" > /tmp/chan.scm guix time-machine --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 \ -C /tmp/chan.scm \ -- package -i pyhton-umap-learn This will fix your initial issue, I guess. > [h...@max-login3.mdc-berlin.net:~] $ guix time-machine > --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 -C /tmp/chan.scm -- > package -p guix/new/.guix-profile -i python-umap-learn I have not checked in your previous email, but it is the wrong commit. > build of > /gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv > failed > View build log at > '/gnu/var/log/guix/drvs/vx/f3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv'. > guix package: error: build of > `/gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv' > failed It could be expected since the package 'python-scikit-learn' is broken: https://data.guix.gnu.org/repository/1/branch/master/package/python-scikit-learn/output-history especially for the commit you are trying (which is not the one you need for the working 'python-umap-learn' package). > Why this commit? 'python-umap-learn' should be broken > > This commit is the most recent succeeded build from 2020-04-18 19:24:20, you > also suggested this commit before. Ah yeah but then what was the previous commit cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523? :-) > [h...@max-login3.mdc-berlin.net:~] $ guix time-machine > --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- help > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... > Updating channel 'guix-bimsb' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb.git'... > Updating channel 'guix-past' from Git repository at > 'https://gitlab.inria.fr/guix-hpc/guix-past'... > Updating channel 'guix-bimsb-nonfree' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb-nonfree.git'... [...] > /builder for > `/gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv' failed > to produce output path > `/gnu/store/9vpcvp00acz4lvglfs1k69a4i05p5hbw-guix-package-cache' > build of /gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv > failed > View build log at > '/gnu/var/log/guix/drvs/ya/j4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv'. > cannot build derivation > `/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv': 1 dependencies > couldn't be built > guix time-machine: error: build of > `/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv' failed This comes from the extra 3 channels you added. If you remove them (see above), then it should work, I guess. Hope that helps, simon
Re: [ext] Re: failed to install the python-umap-learn package
Dear Simon, Now the error is coming from python-scikit-learn-0.20.4. Please find my answers and comments inline. best regards, Hong From: zimoun Sent: 30 September 2020 14:11 To: Li, Hong Cc: Ludovic Courtès; help-guix@gnu.org Subject: Re: [ext] Re: failed to install the python-umap-learn package On Wed, 30 Sep 2020 at 13:41, hong...@mdc-berlin.de wrote: > $ guix time-machine --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 -- > package -p guix/new/.guix-profile -i python3 python-umap-learn > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... > Updating channel 'guix-bimsb' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb.git'... > Updating channel 'guix-past' from Git repository at > 'https://gitlab.inria.fr/guix-hpc/guix-past'... > Updating channel 'guix-bimsb-nonfree' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb-nonfree.git'... [...] > |builder for `/gnu/store/jvffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv' > failed to produce output path > `/gnu/store/gg8fs00h7vqx29icijxpd7w99z1p8lmf-guix-past' > build of /gnu/store/jvffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv failed The error comes from the channel 'guix-past'. Well, I will investigate later... Therefore, you have to turn off this channel. The simplest is to run: echo "%default-channels" > /tmp/chan.scm guix time-machine --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 \ -C /tmp/chan.scm \ -- package -p guix/new/.guix-profile -i python3 python-umap-learn Hope that helps. [h...@max-login3.mdc-berlin.net:~] $ guix time-machine --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 -C /tmp/chan.scm -- package -p guix/new/.guix-profile -i python-umap-learn Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'... guile: warning: failed to install locale guix package: warning: Consider running 'guix pull' followed by 'guix package -u' to get up-to-date packages and security updates. updating substitutes from 'https://ci.guix.gnu.org'... 100.0% The following package will be installed: python-umap-learn0.3.10 /gnu/store/yg68y32h1fhngn8mqpfyc8lzfg25df48-python-umap-learn-0.3.10 substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0% building /gnu/store/fzcysynrdkz52f077c4hbrdmpwkb01nx-python-numba-0.46.0.drv... updating substitutes from 'https://ci.guix.gnu.org'... 100.0% building /gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv... 100% 'check' [###]builder for `/gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv' failed with exit code 1 build of /gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv failed View build log at '/gnu/var/log/guix/drvs/vx/f3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv'. guix package: error: build of `/gnu/store/vxf3qwhkahgzfhwp6c63vm8vky9fj5bl-python-scikit-learn-0.20.4.drv' failed > [h...@max-login3.mdc-berlin.net:~] $ guix time-machine > --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- package -p > guix/new/.guix-profile -i python3 python-umap-learn Why this commit? 'python-umap-learn' should be broken This commit is the most recent succeeded build from 2020-04-18 19:24:20, you also suggested this commit before. > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... > Updating channel 'guix-bimsb' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb.git'... > Updating channel 'guix-past' from Git repository at > 'https://gitlab.inria.fr/guix-hpc/guix-past'... > Updating channel 'guix-bimsb-nonfree' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb-nonfree.git'... > Computing Guix derivation for 'x86_64-linux'... WARNING: (guix build > emacs-build-system): imported module (guix build utils) overrides core > binding `delete'| > The following derivation will be built: >/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv > The following profile hook will be built: >/gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv > building package cache... > /builder for > `/gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv' failed > to produce output path > `/gnu/store/9vpcvp00acz4lvglfs1k69a4i05p5hbw-guix-package-cache' > build of /gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv > failed > View build log at > '/gnu/var/log/guix/drvs/ya/j4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache
Re: [ext] Re: failed to install the python-umap-learn package
On Wed, 30 Sep 2020 at 13:41, hong...@mdc-berlin.de wrote: > $ guix time-machine --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 -- > package -p guix/new/.guix-profile -i python3 python-umap-learn > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... > Updating channel 'guix-bimsb' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb.git'... > Updating channel 'guix-past' from Git repository at > 'https://gitlab.inria.fr/guix-hpc/guix-past'... > Updating channel 'guix-bimsb-nonfree' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb-nonfree.git'... [...] > |builder for `/gnu/store/jvffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv' > failed to produce output path > `/gnu/store/gg8fs00h7vqx29icijxpd7w99z1p8lmf-guix-past' > build of /gnu/store/jvffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv failed The error comes from the channel 'guix-past'. Well, I will investigate later... Therefore, you have to turn off this channel. The simplest is to run: echo "%default-channels" > /tmp/chan.scm guix time-machine --commit=cd5406effa34fa5cfda7eb7bbd2ccaf5201cf523 \ -C /tmp/chan.scm \ -- package -p guix/new/.guix-profile -i python3 python-umap-learn Hope that helps. > [h...@max-login3.mdc-berlin.net:~] $ guix time-machine > --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- package -p > guix/new/.guix-profile -i python3 python-umap-learn Why this commit? 'python-umap-learn' should be broken > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... > Updating channel 'guix-bimsb' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb.git'... > Updating channel 'guix-past' from Git repository at > 'https://gitlab.inria.fr/guix-hpc/guix-past'... > Updating channel 'guix-bimsb-nonfree' from Git repository at > 'https://github.com/BIMSBbioinfo/guix-bimsb-nonfree.git'... > Computing Guix derivation for 'x86_64-linux'... WARNING: (guix build > emacs-build-system): imported module (guix build utils) overrides core > binding `delete'| > The following derivation will be built: >/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv > The following profile hook will be built: >/gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv > building package cache... > /builder for > `/gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv' failed > to produce output path > `/gnu/store/9vpcvp00acz4lvglfs1k69a4i05p5hbw-guix-package-cache' > build of /gnu/store/yaj4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv > failed > View build log at > '/gnu/var/log/guix/drvs/ya/j4m68r6l9jhdb767psz79fm84hb6x6-guix-package-cache.drv'. > cannot build derivation > `/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv': 1 dependencies > couldn't be built I do not know why it returns an error here. What happens if you run: guix time-machine --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- help ? All the best, simon
Re: [ext] Re: failed to install the python-umap-learn package
/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv' failed best regards, Hong From: Ludovic Courtès Sent: 30 September 2020 10:56:24 To: zimoun Cc: Li, Hong; help-guix@gnu.org Subject: [ext] Re: failed to install the python-umap-learn package Hi, zimoun skribis: > Thank you for pointing out the issue. Using the Guix Data Service, > > > https://data.guix.gnu.org/repository/1/branch/master/package/python-umap-learn/output-history [...] > From the Guix Data Service, the first offending commit is > cac674d99dc4a332e6210c57ec7f1b8164f66642 which updates python-cython. Neat! We should put that that to good use somehow to quickly notice and fix regressions: with IRC/email notifications, ‘guix weather’ reporting info from the Data Service, things like that. Ludo’.
Re: failed to install the python-umap-learn package
Hi, zimoun skribis: > Thank you for pointing out the issue. Using the Guix Data Service, > > > https://data.guix.gnu.org/repository/1/branch/master/package/python-umap-learn/output-history [...] > From the Guix Data Service, the first offending commit is > cac674d99dc4a332e6210c57ec7f1b8164f66642 which updates python-cython. Neat! We should put that that to good use somehow to quickly notice and fix regressions: with IRC/email notifications, ‘guix weather’ reporting info from the Data Service, things like that. Ludo’.
Re: failed to install the python-umap-learn package
Dear Hong Li, On Tue, 29 Sep 2020 at 16:09, Ludovic Courtès wrote: > "hong...@mdc-berlin.de" skribis: > > > I had a failure when installing python-umap-learn in guix. It took very > > long time in the 'check' phase. Usually, if "guix weather python-umap-learn" says that there is no substitute, then it is a bad sign. :-) > > The error does not change before and after 'guix pull'. Could you please > > tell me how to solve this problem? Thank you for pointing out the issue. Using the Guix Data Service, https://data.guix.gnu.org/repository/1/branch/master/package/python-umap-learn/output-history one can see the versions which build and the ones which fail (mainly because dependencies, apparently). One the last Succeeded row, you can click on the revision 2020-04-18 19:24:20 which indicates the last known commit where python-umap-learn builds. Therefore, you can run: guix time-machine --commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 \ -- package -i pyhton-umap-learn Hope that helps. > It would seem that one of the tests of python-numba is failing, perhaps > in a non-deterministic way. >From the Guix Data Service, the first offending commit is cac674d99dc4a332e6210c57ec7f1b8164f66642 which updates python-cython. All the best, simon
Re: failed to install the python-umap-learn package
Hi, "hong...@mdc-berlin.de" skribis: > I had a failure when installing python-umap-learn in guix. It took very long > time in the 'check' phase. > > The error does not change before and after 'guix pull'. Could you please tell > me how to solve this problem? > > Thanks in advance! Please see the screen output below: > > > $ guix package -i python-umap-learn > > The following package will be installed: >python-umap-learn 0.3.10 > > The following derivations will be built: >/gnu/store/4sbifbl79yy6xnbnkvj0hvc3i2mp6jcj-python-umap-learn-0.3.10.drv >/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv > building > /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv... > - 'check' phasebuilder for > `/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv' failed > with exit code 1 > build of /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv > failed > View build log at > '/gnu/var/log/guix/drvs/ra/7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv'. > guix package: error: build of > `/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv' failed It would seem that one of the tests of python-numba is failing, perhaps in a non-deterministic way. As a stopgap, you should be able to run: guix install python-umap-learn --without-tests=python-numba Note that ‘--without-tests’ was added just a couple of days ago, so you may need to run ‘guix pull’ to get a recent-enough Guix: https://guix.gnu.org/manual/devel/en/html_node/Package-Transformation-Options.html HTH, Ludo’.
failed to install the python-umap-learn package
Dear developers, I had a failure when installing python-umap-learn in guix. It took very long time in the 'check' phase. The error does not change before and after 'guix pull'. Could you please tell me how to solve this problem? Thanks in advance! Please see the screen output below: $ guix package -i python-umap-learn The following package will be installed: python-umap-learn 0.3.10 The following derivations will be built: /gnu/store/4sbifbl79yy6xnbnkvj0hvc3i2mp6jcj-python-umap-learn-0.3.10.drv /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv building /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv... - 'check' phasebuilder for `/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv' failed with exit code 1 build of /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv failed View build log at '/gnu/var/log/guix/drvs/ra/7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv'. guix package: error: build of `/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv' failed $ guix package -i python-numba The following package will be installed: python-numba 0.46.0 The following derivation will be built: /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv building /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv... - 'check' phasebuilder for `/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv' failed with exit code 1 build of /gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv failed View build log at '/gnu/var/log/guix/drvs/ra/7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv'. guix package: error: build of `/gnu/store/ra7xx13ni736p0kvcsbhsl0g9yhy4d68-python-numba-0.46.0.drv' failed $ guix -V guix (GNU Guix) 90492a9f13b4b8eaa6025d5a18e0b130cf257dbe best regards, Hong
