Re: [ext] Re: failed to install the python-umap-learn package

2020-09-30 Thread hong...@mdc-berlin.de
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


Installing gcc debugging symbols?

2020-09-30 Thread Simon South
Is there a way to install debugging information for gcc, as one can for
glibc and other packages?

I'm trying to test a change to Knot 3.0.0 and have found that gcc takes
forever to finish linking (and usually crashes from running out of
memory) when building the package using "guix build knot". Meanwhile, if
I build the source "manually", from within "guix environment --pure
knot", everything works fine.

I'd like to diagnose this but connecting to the running gcc instance
using gdb doesn't reveal much without gcc's debugging information
available.

I've tried "guix install gcc-toolchain@7.5:debug" but that installs
debugging information for only glibc.

I could edit gnu/packages/gcc.scm to set the "stripped?" variable to
false and rebuild gcc so its debugging symbols are preserved, but then
it's not clear how to install them. It seems I can build and install gcc
itself with

  guix package --install-from-expression='(@ (gnu packages gcc) gcc-7)'

but what I really want is

  guix package --install-from-expression='(@ (gnu packages gcc) (list gcc-7 
"debug"))'

This fails with a syntax error, however, and I see the documentation for
"guix package" says

   Note that this option installs the first output of the specified
   package, which may be insufficient when needing a specific output of
   a multiple-output package.

Is there a trick to making this work?

-- 
Simon South
si...@simonsouth.net



Re: [ext] Re: failed to install the python-umap-learn package

2020-09-30 Thread zimoun
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



Helvetica in `guix graph`

2020-09-30 Thread Fulbert
  Hi Guixers,

  When I pipe `guix graph hello | xdot -`, the characters are
displayed as squares. Got to insert
`… | sed "s/Helvetica/sans/g" | …` in the pipeline.

  Not sure if this is a bug. Maybe my system should find a
substitute for "Helvetica" automatically ?

  … or maybe line 241 of 'guix/graph.scm' needs a tiny correction ?

(format port "  \"~a\" [label = \"~a\", shape = box, fontname = Helvetica];~%" 
id label))


  Best regards,
  Fulbert



Re: [ext] Re: failed to install the python-umap-learn package

2020-09-30 Thread hong...@mdc-berlin.de
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.drv'.
> cannot build derivation 
> `/gnu/store/zz2557r32hsq2ksa53ix4ygaskkrs2qi-profile.drv': 1 dependencies 
> couldn't be built

I do 

Re: [ext] Re: failed to install the python-umap-learn package

2020-09-30 Thread zimoun
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

2020-09-30 Thread hong...@mdc-berlin.de
Dear Ludo and Simon,


Thanks for the reply.

Unfortunately, I still have errors to install python-umap-learn package 
(dependencies error), see messages below:


$ 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'...
substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
The following derivations will be built:
   /gnu/store/6h3y0lp2mg8rlqbaam26n8dn6yfafrv7-compute-guix-derivation.drv
   /gnu/store/dfglc6l495466asp04ajwqlqdi2bgn6d-module-import-compiled.drv
   /gnu/store/zgi9gikccaa882a8amivvc0wlc7x610i-module-import.drv
building /gnu/store/zgi9gikccaa882a8amivvc0wlc7x610i-module-import.drv...
building 
/gnu/store/dfglc6l495466asp04ajwqlqdi2bgn6d-module-import-compiled.drv...
building 
/gnu/store/6h3y0lp2mg8rlqbaam26n8dn6yfafrv7-compute-guix-derivation.drv...
Computing Guix derivation for 'x86_64-linux'... /
substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
The following derivations will be built:
   /gnu/store/fqaf4nrmvyjclisrf4b8chx0idlm1xrv-profile.drv
   /gnu/store/c718qi7pdrzshrppv03v91sf6057j5fm-guix-bimsb-nonfree.drv
   /gnu/store/fh3306a50cnh1l6y6dij2l6243d6cvc2-inferior-script.scm.drv
   /gnu/store/flj6npydjr8fxv3g30qfw4gxsg77q48a-guix-bimsb.drv
   /gnu/store/z4ckz3745wzng8bn53n22kc0ib3h61p8-inferior-script.scm.drv
   /gnu/store/jvffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv
   /gnu/store/ydj320kw2ylvkkzvs39nn1qsy5ykpmvw-module-import-compiled.drv
   /gnu/store/p7727k2lldx5s2h2kr71i74999np2pl2-module-import-compiled.drv
   /gnu/store/xzzd9bvs0rm71clvrbpk937hban06yh2-inferior-script.scm.drv
   /gnu/store/y7vc292wihdzias98dyzxfbnd24szc04-profile.drv
The following profile hooks will be built:
   /gnu/store/fv1gghy2a7m3s6bbpal32xbl8dfnw5dz-ca-certificate-bundle.drv
   /gnu/store/lz2s0p1k6ppjc0mjrq8ylcb82f2bwwif-guix-package-cache.drv
   /gnu/store/pq81nf3xdhkbrmfaig1m2mc0h0519ygl-info-dir.drv
   /gnu/store/s638gz72pfazskd3j0l5labcfkgnxz44-fonts-dir.drv
   /gnu/store/x43hvdc1rrsqhi6zy5p9wn8g1la2rw1x-manual-database.drv
building /gnu/store/jvffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv...
|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
View build log at 
'/gnu/var/log/guix/drvs/jv/ffmvaz1rm0q11c57wmsp08h0slj9ym-guix-past.drv'.
cannot build derivation 
`/gnu/store/fqaf4nrmvyjclisrf4b8chx0idlm1xrv-profile.drv': 1 dependencies 
couldn't be built
guix time-machine: error: build of 
`/gnu/store/fqaf4nrmvyjclisrf4b8chx0idlm1xrv-profile.drv' failed
[h...@max-login3.mdc-berlin.net:~] $ guix time-machine 
--commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- 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'...
^C
[h...@max-login3.mdc-berlin.net:~] $ guix time-machine 
--commit=cac674d99dc4a332e6210c57ec7f1b8164f66642 -- 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'...
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
guix time-machine: error: build of 

Re: failed to install the python-umap-learn package

2020-09-30 Thread Ludovic Courtès
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: guix system reconfigure fails

2020-09-30 Thread luhux
On Tue, Sep 29, 2020 at 10:34:11PM +, Abraham Jose wrote:
> Git error: SSL error: received early EOF

This may be your network problem

You may be able to copy the git repository locally and then:

guix pull --url=/path/to/guix




Re: Fonts do not work with multiple profiles (fontconfig) and a proposed workaround

2020-09-30 Thread Todor Kondić
> Hi Todor,
>
> Indeed, this workaround does the trick.
> Here is my ~/.config/fontconfig/fonts.conf:
>
> --8<---cut here---start->8---
> 
> 
> 
> 
> ~/.guix-extra-profiles/emacs/emacs/share/fonts
> 
> --8<---cut here---end--->8---
>
> Packages' content is static, it is not modifier upon install, which is
> why the default etc/fonts/fonts.conf is pointing to constant locations.
>
> The solution to this bug, I believe, would be to add a post-install
> hook that generates the fonts.conf file with the right entries.
>
> Cheers!
>
> ---
>
> Pierre Neidhardt
> https://ambrevar.xyz/

Hi Pierre,

Yes, of course you are right. Packages are installed once and then reused in 
different profiles (AFAIK). I just did not give much thought to it at the 
moment. Supporting multiple profiles in a package can be a real pain, right? I 
mean, there is no magic bullet. In the case of fontconfig, we have the ability 
to modify the fonts.conf in order to add more font paths. As for other 
programs, there is usually a way, but it is not universal.

Of course, the hammer solution would be to shove a package going into a 
different profile into a different store entry (under assumption that at the 
build-time the package takes -p option as the default). Perhaps something like 
that could be offered as an option to users? Maybe this is even possible now? I 
have not done any research on it.

On the other hand, I have not seen any real "official" endorsement of 
multi-profile setups by Guix as a project :) .

Cheers,

T