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License: GNU General Public License v3.0
Free scientific packages for GNU Guix.
License: GNU General Public License v3.0
Hello,
I have an error installing bazel with the latest guix-science:
# guix install bazel
The following package will be installed:
bazel 6.4.0
substitute: guile: warning: failed to install locale
The following derivation will be built:
/gnu/store/84535qg03i8vyspvrys9lnkaxpcxj8jp-bazel-6.4.0.drv
guile: warning: failed to install locale
building /gnu/store/84535qg03i8vyspvrys9lnkaxpcxj8jp-bazel-6.4.0.drv...
| 'build' phasebuilder for `/gnu/store/84535qg03i8vyspvrys9lnkaxpcxj8jp-bazel-6.4.0.drv' failed with exit code 1
build of /gnu/store/84535qg03i8vyspvrys9lnkaxpcxj8jp-bazel-6.4.0.drv failed
View build log at '/var/log/guix/drvs/84/535qg03i8vyspvrys9lnkaxpcxj8jp-bazel-6.4.0.drv.bz2'.
guix install: error: build of `/gnu/store/84535qg03i8vyspvrys9lnkaxpcxj8jp-bazel-6.4.0.drv' failed
The build log contains this error:
starting phase `build'
error: in phase 'build': uncaught exception:
%exception #<&invoke-error program: "proot" arguments: ("-b" "/gnu/store/rln3p3ds89wv3cww1jimcvhd2kg7qsvw-bash-static-5.1.16/bin/bash:/bin/bash" "-b" "/gnu/store/yr39rh6wihd1wv6gzf7w4w687dwzf3vb-coreutils-9.1/bin/env:/usr/bin/env" "bash" "compile.sh") exit-status: 255 term-signal: #f stop-signal: #f>
phase `build' failed after 0.1 seconds
command "proot" "-b" "/gnu/store/rln3p3ds89wv3cww1jimcvhd2kg7qsvw-bash-static-5.1.16/bin/bash:/bin/bash" "-b" "/gnu/store/yr39rh6wihd1wv6gzf7w4w687dwzf3vb-coreutils-9.1/bin/env:/usr/bin/env" "bash" "compile.sh" failed with status 255
Here are my current channels:
Generation 37 Jan 29 2024 10:58:58 (current)
guix 2c5293a
repository URL: https://git.savannah.gnu.org/git/guix.git
branch: master
commit: 2c5293afffa39d5d4aaec248a1973c7f62b1a0b4
guix-science 0b3d4a2
repository URL: https://github.com/guix-science/guix-science.git
branch: master
commit: 0b3d4a2f6d72c24f169bd5bf663f920ede5a8ae9
guix-hpc-non-free f4b5bab
repository URL: https://gitlab.inria.fr/guix-hpc/guix-hpc-non-free.git
branch: master
commit: f4b5babaafb10e18ea634fac349d014a3a9fd6b0
guix-science-nonfree 875054b
repository URL: https://github.com/guix-science/guix-science-nonfree.git
branch: master
commit: 875054b1c528088a6b8c38fed92b83a10f20075b
guix-past d60a388
repository URL: https://gitlab.inria.fr/guix-hpc/guix-past
branch: master
commit: d60a388678098e6de60ca1a65806903b5739da29
guix-hpc a494779
repository URL: https://gitlab.inria.fr/guix-hpc/guix-hpc.git
branch: master
commit: a49477909d49a12ec9e32d1e8a552a665e2135da
Thanks in advance for your help
Emmanuel Medernach
Openssl-1.0 was just removed from Guix. guix-past still has openssl-1.0 but I don't know if guix-science should depend on it. Or if there's a newer version of grid-engine-core which can use a newer openssl.
Hi,
Just installed python-jupyterlab and seems to be working - I did notice that when creating a notebook - be it python or guix-jupyter based, that the stdout from jupyter lab
have a bunch of read-only errors with what looks like the webserver trying to write into the gnu store.
Things seems to be working OK despite this, but was wondering if this was a known issue, or unique to my setup? Do I have to pass in some custom config to point to writable locations?
$ guix describe
Generation 32 Oct 03 2021 17:54:26 (current)
guix c98c9c5
repository URL: https://git.savannah.gnu.org/git/guix.git
branch: master
commit: c98c9c514261d7e870e9eb13673a3faaa46b998d
guix-science b574aa6
repository URL: https://github.com/guix-science/guix-science.git
branch: master
commit: b574aa67743cd4f138fd32efb7c116342f360625
nonguix 3246eac
repository URL: https://gitlab.com/nonguix/nonguix
branch: master
commit: 3246eac4fe6d7cab88ea21d9de902caf4aa6e522
guix environment --ad-hoc python-jupyterlab guix-jupyter
jupyter lab
[I 18:14:29.958 LabApp] Kernel started: bd86ce25-41e2-4388-9b8d-4ea7011199d5, name: guix
[W 18:14:30.192 LabApp] 500 PUT /lab/api/workspaces/lab?1633281270190 (127.0.0.1): [Errno 30] Read-only file system: '/gnu/store/9zikasyb62q8b4v3c2n6qgl55dw7hfm2-profile/etc/jupyter/lab'
[W 18:14:30.192 LabApp] [Errno 30] Read-only file system: '/gnu/store/9zikasyb62q8b4v3c2n6qgl55dw7hfm2-profile/etc/jupyter/lab'
[E 18:14:30.193 LabApp] {
"Host": "localhost:8888",
"User-Agent": "Mozilla/5.0 (X11; Linux x86_64; rv:92.0) Gecko/20100101 Firefox/92.0",
"Accept": "*/*",
"Accept-Language": "en-US,en;q=0.5",
"Accept-Encoding": "gzip, deflate",
"Referer": "http://localhost:8888/lab",
"Content-Type": "text/plain;charset=UTF-8",
"Authorization": "token 8564806bac3445d88d7e276cd97c6f818a9b990b7e00f8e6",
"X-Xsrftoken": "2|dbdf2c34|4f331bd49e9b9b1b1227835e10bb26de|1634216059",
"Origin": "http://localhost:8888",
"Content-Length": "521",
"Connection": "keep-alive",
"Cookie": "username-localhost-8888=\"2|1:0|10:1634216059|23:username-localhost-8888|44:MjPjYzAzZDRkYmRiPGJhMWIyYWI5Kzhj3DY5NWY1ZGI=|38e4779f2a4f67c75c79f15de5e241b0ac25f45f3e8c9e337189076bb26a4f41\"; _xsrf=2|dbdf2c34|4f331bd49e9b9b1b1227835e10bb26de|1634216059",
"Sec-Fetch-Dest": "empty",
"Sec-Fetch-Mode": "cors",
"Sec-Fetch-Site": "same-origin",
"Pragma": "no-cache",
"Cache-Control": "no-cache"
}
[E 18:14:30.193 LabApp] 500 PUT /lab/api/workspaces/lab?1634216059 (127.0.0.1) 1.300000ms referer=http://localhost:8888/lab
guix[17816]: Guix kernel started (PID 16816)
Just released, see notes https://rstudio.com/products/rstudio/release-notes/
There is an experimental package in branch rstudio-1.4
, but it depends on the Guix branch wip-node-14
(specifially the new node-build-system).
Hi, first thank you for this channel!
I recently installed Rstudio from this channel, but I can’t use it because the panes don’t show any text. Only in the menu bar the texts appear. See below.
I’ve tried to change rendering settings or disable gpu (according Rstudio community for blank screen bug), and install several fonts to default system but the error persists.
I have GuixSD 1.3.
I just tried to add guix-science channel. It is not working, because python2-numpy is not defined in guix.
This is from the guix error log:
(exception unbound-variable (value #f)
(value "Unbound variable: ~S")
(value (python2-numpy))
(value #f))
This might be feasible to include in guix proper, but I am wondering if you would be able to provide the r-tesseract
package. tesseract-ocr
in Guix also seems outdated relative to the needs of the R package.
Below I offer my pathetic attempt towards this goal. I could get the tesseract-ocr
package to build by not exposing their Makefile to asciidoc and docbook stuff. I could also get the r-tesseract
package to build on top of it. Unfortunately, the package fails to load in R since it cannot find any language training data.
(use-modules (guix packages)
(guix download)
(guix build-system gnu)
(gnu packages compression)
(gnu packages xml)
(gnu packages gtk)
(gnu packages backup)
(gnu packages curl)
(gnu packages icu4c)
(gnu packages image)
(gnu packages python)
(gnu packages documentation)
(gnu packages autotools)
; (gnu packages docbook)
(guix build-system r)
(guix git-download)
((guix licenses) #:prefix license:)
(gnu packages pkg-config)
(gnu packages cran)
(gnu packages ocr)
(gnu packages graph)
(gnu packages statistics)
(gnu packages gcc))
(define-public tesseract-ocr5.1
;; There are useful commits beyond the last official stable release.
(let ((commit "c2a3efe2824e1c8a0810e82a43406ba8e01527c4")
(revision "1"))
(package
(name "tesseract-ocr5.1")
(version (git-version "5.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tesseract-ocr/tesseract")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"11asiy9zbmhp8x1xlqiv7a22nhac1xviw03gn2mpsjpx3b1pfp07"))))
(build-system gnu-build-system)
(inputs
`(("cairo" ,cairo)
("icu" ,icu4c)
("leptonica" ,leptonica)
("pango" ,pango)
("python-wrapper" ,python-wrapper)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libarchive" ,libarchive)
("libcurl" ,curl)
("libtool" ,libtool)
("libtiff" ,libtiff)
("pkg-config" ,pkg-config)
("xsltproc" ,libxslt)))
(arguments
`(#:configure-flags
(let ((leptonica (assoc-ref %build-inputs "leptonica")))
(list (string-append "LIBLEPT_HEADERSDIR=" leptonica "/include")))
#:tests? #f ; Tests currently result in a segfault
#:phases
(modify-phases %standard-phases
(add-after 'install 'build-training
(lambda _
(invoke "make" "training")))
(add-after 'build-training 'install-training
(lambda _
(invoke "make" "training-install"))))))
(home-page "https://github.com/tesseract-ocr/tesseract")
(synopsis "Optical character recognition engine")
(description
"Tesseract is an optical character recognition (OCR) engine with very
high accuracy. It supports many languages, output text formatting, hOCR
positional information and page layout analysis. Several image formats are
supported through the Leptonica library. It can also detect whether text is
monospaced or proportional.")
(license license:asl2.0))))
I can't say ignoring the documentation is the best practice, but I was just hoping to be able to use the R package...
(define-public r-tesseract
(package
(name "r-tesseract")
(version "5.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tesseract" version))
(sha256
(base32 "1xdwjm3bing15ljdicl20g88ymmd0bbjmlbah5hzvws5b656iicn"))))
(properties `((upstream-name . "tesseract")))
(build-system r-build-system)
(inputs (list zlib))
(propagated-inputs (list r-curl r-digest r-pdftools r-rappdirs r-rcpp))
(native-inputs (list pkg-config r-knitr tesseract-ocr5.1 leptonica))
(home-page
"https://docs.ropensci.org/tesseract/https://github.com/ropensci/tesseract")
(synopsis "Open Source OCR Engine")
(description
"Bindings to 'Tesseract' <https://opensource.google/projects/tesseract>: a
powerful optical character recognition (OCR) engine that supports over 100
languages. The engine is highly configurable in order to tune the detection
algorithms and obtain the best possible results.")
(license license:gpl2)))
Here is the text of the error I saw in R when loading:
Error opening data file /gnu/store/ihga2gkalxzfmbaczaf5xazdqbc5h4ly-tesseract-ocr5.1-5.1.0-1.c2a3efe/share/tessdata/eng.traineddata
Please make sure the TESSDATA_PREFIX environment variable is set to your "tessdata" directory.
Failed loading language 'eng'
Tesseract couldn't load any languages!
Warning message:
Unable to find English training data
I looked in that gnu/store
directory and sure enough there was no trained data. I also didn't see any evidence that you could download language training data from Guix either.
I originally had an older version of r-tesseract
in my personal channel which seems to be circa the same period as Guix's tesseract-ocr package, but sadly that now fails to build.
(define-public r-tesseract
(package
(name "r-tesseract")
(version "4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tesseract" version))
(sha256
(base32
"1a7cf48n7hdd6inqz23ifqhq6kx6wxri34a79ns2vxaj6f4llxf0"))))
(properties `((upstream-name . "tesseract")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)
("tesseract-ocr" ,tesseract-ocr)
("leptonica" ,leptonica)))
(propagated-inputs
`(("r-curl" ,r-curl)
("r-digest" ,r-digest)
("r-pdftools" ,r-pdftools)
("r-rappdirs" ,r-rappdirs)
("r-rcpp" ,r-rcpp)))
(native-inputs
`(("pkg-config" ,pkg-config)
("r-knitr" ,r-knitr)))
(home-page
"https://github.com/ropensci/tesseract")
(synopsis "Open Source OCR Engine")
(description
"Bindings to 'Tesseract' <https://opensource.google.com/projects/tesseract>: a powerful optical character recognition (OCR) engine that supports over 100 languages. The engine is highly configurable in order to tune the detection algorithms and obtain the best possible results.")
(license license:asl2.0)))
New release v1.4.1717 is out, see release notes.
Set up a server that provides substitutes.
python-jaxlib 0.4.20 bazel deps gives wrong hash on aarch64
Trying to update a container definition involving python-jupyterlab
from guix-science
today, I hit a weird build error:
guix time-machine -C channels.scm -- shell -C -N -m manifest.scm jupyterlab
ends with:
building /gnu/store/ilj86384yh5v6fbllnc1hv0scy09372m-guix-science.drv...
-builder for `/gnu/store/ilj86384yh5v6fbllnc1hv0scy09372m-guix-science.drv' failed to produce output path `/gnu/store/59krkb7s89g830is9ig2j4bi22wd6cmp-guix-science'
build of /gnu/store/ilj86384yh5v6fbllnc1hv0scy09372m-guix-science.drv failed
View build log at '/var/log/guix/drvs/il/j86384yh5v6fbllnc1hv0scy09372m-guix-science.drv.bz2'.
The build log says:
(repl-version 0 1 1)
WARNING: (guix-science build bazel-build-system): imported module (guix build utils) overrides core binding `delete'
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (python-nr-stream)) (value #f))
which I don't understand at all.
My channels.scm
is:
(list (channel
(name 'guix)
(url "https://git.savannah.gnu.org/git/guix.git")
(branch #f)
(commit
"5149bf99ba0238b647733399b1a9cbf7da486634")
(introduction
(make-channel-introduction
"9edb3f66fd807b096b48283debdcddccfea34bad"
(openpgp-fingerprint
"BBB0 2DDF 2CEA F6A8 0D1D E643 A2A0 6DF2 A33A 54FA"))))
(channel
(name 'guix-science)
(url "https://github.com/guix-science/guix-science.git")
(commit
"2da76d86b13ac5ae8fdb7ddd9df76a9212b8e2c2")
(introduction
(make-channel-introduction
"b1fe5aaff3ab48e798a4cce02f0212bc91f423dc"
(openpgp-fingerprint
"CA4F 8CF4 37D7 478F DA05 5FD4 4213 7701 1A37 8446")))))
and the manifest:
(specifications->manifest
(list "python-jupyterlab"
"python" "python-numpy" "python-scipy"
"python-scikit-image" "python-fitsio"
"python-requests"
"python-pandas"
"python-statsmodels"
"nss-certs"
"openssl"))
I authorized the key and explicitly passed the substitute server on the command line, but RStudio is still being built from source.
Is there a public Cuirass frontend where build logs could be checked, so users could have some sense of whether the build failed or if it's pending?
The build of rstudio-2021.09.2+382 in the channel failed in the "configure" phase. This also happens on the substitute server https://guix.bordeaux.inria.fr/. The last successful build was on 15 July.
Relevant logs can be viewed at https://guix.bordeaux.inria.fr/search?query=rstudio-2021.09.2%20382&border-low-id=15000
I had originally posted this in guix-science-nonfree where it was brought to my attention that GATK is now free software. I have been having a bit of trouble packaging it and would appreciate help from someone with a little more experience. Here is what my package definition looks like thus far:
(define-public gatk
(package
(name "gatk")
(version "4.4.0.0")
(source (origin
(method url-fetch)
(uri
(string-append "https://github.com/broadinstitute/gatk/releases/download/" version "/gatk-" version ".zip"))
(sha256
(base32
"1453l72cfwqw5y3na0d520czzq11x46d9dq66q5ssilbngvh0ij4"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; This is a binary package only, so no tests.
#:phases
(modify-phases %standard-phases
(delete 'configure) ; Nothing to configure.
(delete 'build) ; This is a binary package only.
(replace 'install
(lambda _
(let ((out (string-append (assoc-ref %outputs "out")
"/share/java/" ,name "/")))
(mkdir-p out)
(copy-recursively (assoc-ref %build-inputs "source")
(string-append out "/"))))))))
(native-inputs
(list
unzip))
(propagated-inputs
(list
r-gsalib
r-ggplot2
r-gplots
r-reshape
r-optparse
r-dnacopy
r-naturalsort
r-dplyr
r-data-table
r-hmm
))
(home-page "https://www.broadinstitute.org/gatk/")
(synopsis "Package for analysis of high-throughput sequencing")
(description "The Genome Analysis Toolkit or GATK is a software package for
analysis of high-throughput sequencing data, developed by the Data Science and
Data Engineering group at the Broad Institute. The toolkit offers a wide
variety of tools, with a primary focus on variant discovery and genotyping as
well as strong emphasis on data quality assurance. Its robust architecture,
powerful processing engine and high-performance computing features make it
capable of taking on projects of any size.")
;; There are additional restrictions that make it nonfree.
(license license:expat)))
I have modeled this after the GATK 3.8 package which previously existed in guix-science-nonfree. I think that all I need to do in the install step is to copy the entire unarchived directory to the output directory, but I am receiving the following error:
error: in phase 'install': uncaught exception:
system-error "copy-file" "~A" ("Is a directory") (21)
phase `install' failed after 0.0 seconds
I had thought copy-recursively
should work here, but perhaps I am mistaken.
Also, I would be happy to submit a merge request for this package once it is working, if that would be desired.
When installing RStudio and R in a new profile with guix package --profile=/what/ever -i rstudio -i r
it fails to find R's home and quits with an error popup.
Since I only started using R a week ago I'm not really keen to be the one to debug this, but I can run whatever diagnostics yall need.
JupyterLab 3 is out, changelog.
See https://github.com/guix-science/guix-science/tree/jupyter-update for WIP packages
Hi again,
the python-jupyterhub-ldapauthenticator
is affected by the same issue #18.
Could you please fix this also?
Thanks
Dan
There are some CRAN packages, which really shouldn't be in guix-science but in Guix proper instead.
The following packages don't seem to have any dependency on packages that cannot be upstreamed:
We should move those packages to Guix and prevent fine CRAN packages from being added to guix-science needlessly.
Hey guys,
I'm trying to install python-jupyterhub
- fresh profile, but I get the next error:
$ guix package -p jupyterhub-guix -i python-jupyterhub The following package will be installed: python-jupyterhub 1.4.1 guix package: error: profile contains conflicting entries for python-tornado guix package: error: first entry: [email protected] /gnu/store/i23vy8nixgk2dfchj444p1x1sxjh9pxf-python-tornado-5.1.1 guix package: error: ... propagated from [email protected] guix package: error: second entry: [email protected] /gnu/store/ihlxpxpxxqzmq5alpd4f5kbwn3idpf8a-python-tornado-6.1 guix package: error: ... propagated from [email protected] guix package: error: ... propagated from [email protected] hint: You cannot have two different versions or variants of python-jupyterhub in the same profile.
The output of the guix describe
is below:
$ guix describe Generation 6 Aug 29 2022 20:49:21 (current) guix 9529384 repository URL: https://git.savannah.gnu.org/git/guix.git branch: master commit: 9529384c92e6427e7d277ffaa391405ef6ab22f3 guix-science 948c6a3 repository URL: https://github.com/guix-science/guix-science.git branch: master commit: 948c6a3273e84c2ffc929576a5483ba34cf24074
Could you please check and fix this error?
Thank you
Dan
When installing rstudio into a new or ad-hoc environment, or when updating in an existing environment, the build of several node packages seem to fail.
Any ideas on how to fix this?
Terminal log:
(base) [cvermeulen@n0034 ~]$ guixr environment --ad-hoc r rstudio
substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
The following derivations will be built:
/gnu/store/l8dhppcl9m34zik5yyvr9s4bm98qflag-rstudio-1.4.1106.drv
/gnu/store/0j2bsk3zmqfqv1cywisq9kx7drsks3a4-node-react-16.14.0.drv
/gnu/store/sqwfs6r5nqcz58hxa84zpmdzk8vmngyv-node-prop-types-15.7.2.drv
/gnu/store/2ppvwxvfw4sl3fxihwhxi3kjvyyb8c6f-node-react-dock-0.2.4.drv
/gnu/store/q4a35m77q9byfwvzcmnml9aq7n7x0ayg-node-react-17.0.1.drv
/gnu/store/70k3yidsjlnxpvc2bnw30nzgip10x8qg-node-react-dom-16.14.0.drv
/gnu/store/hj9rbknkrw0bzm8ih6mlqk23wf233wcw-node-scheduler-0.19.1.drv
/gnu/store/dj771hd4w994mzdydmjpdssqpmk1aidv-node-fuse-box-3.7.1.drv
/gnu/store/86ri17ngh1n2bams9g46q81y38sazaa2-node-express-4.17.1.drv
/gnu/store/jd5g2883hxczbppgvvqjs0nmkwaw7210-node-send-0.17.1.drv
/gnu/store/pfqra710n7h3wgi1r397scw4bcn0nq99-node-serve-static-1.14.1.drv
/gnu/store/9hz2c8k6bbcqcjjnbc0r0mp7l1q4340x-node-regexpu-core-4.7.1.drv
/gnu/store/y9rhlrgynbydw57l4ld1z3ynfppy6r5x-node-regjsparser-0.6.7.drv
/gnu/store/h9igd3nz98cishwrg7ggi7haayyjam4c-node-realm-utils-1.0.9.drv
/gnu/store/hcji9vnr4ymxib0chcm3jm4q2f9v16rs-node-escodegen-1.14.3.drv
/gnu/store/hycdcps5p1jsqwi8ldfx7d11gn9ccgcy-node-chokidar-1.7.0.drv
/gnu/store/wz9v6pf6ibyrm6cv5shrg19kcqlzbqpg-node-readdirp-2.2.1.drv
/gnu/store/mw8m2lncnpfdklxpd33x7xxmhjg6p2wa-node-micromatch-3.1.10.drv
/gnu/store/0z93b6xfzkq2011b9pzcmcscxz5lz8pk-node-snapdragon-0.8.2.drv
/gnu/store/xxvkklvjhicv6mdp02mj2xx2h9f92s95-node-source-map-resolve-0.5.3.drv
/gnu/store/6qah7ry9kd0vcknd3b21an45ff01pqak-node-extglob-2.0.4.drv
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cannot build derivation `/gnu/store/l8dhppcl9m34zik5yyvr9s4bm98qflag-rstudio-1.4.1106.drv': 1 dependencies couldn't be built
guix environment: error: build of `/gnu/store/l8dhppcl9m34zik5yyvr9s4bm98qflag-rstudio-1.4.1106.drv' failed
Basically the title, Zotero is FLOSS with the GNU AGPL license, so I'm hoping we can add it to this repo, since I've just migrated to guix, and zotero is by far the best reference manager IMO.
I'm not sure how useful I could be, but I'm more than willing to give it a shot to help with the packaging etc.
Do you think this would be the place to ask, or should I ask the guix/non-guix channels instead?
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