Closed mboisson closed 2 years ago
What is the error message?
On Thu, Feb 3, 2022 at 3:50 PM Maxime Boissonneault < @.***> wrote:
Hi, I was asked to build this software for our cluster. However,
- The build procedure does not work
- We already have all of the third parties
Are there instructions on how to build and install this tool without building all of the vendored dependencies ?
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So, if we let aside that the make
command downloads stuff (it should not, make
is supposed to be runnable offline, without any internet connection), and builds stuff that is already available (such as zstd
, tabix
, sqlite
, nlopt
, gsl
, openblas
, pcre
, samtools
), without proper optimizations (we build all of those, but in paritulcar BLAS implementations with specific optimizations for the architectures we run on, for example), it fails in particular with Eigen (which we ALSO have):
echo "obtain Eigen..."
obtain Eigen...
wget --no-check-certificate http://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2 -O eigen-3.3.7.tar.bz2
URL transformed to HTTPS due to an HSTS policy
--2022-02-03 22:11:11-- https://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2
Résolution de bitbucket.org… 104.192.141.1, 2406:da00:ff00::3403:4be7, 2406:da00:ff00::22cd:e0db, ...
Connexion à bitbucket.org|104.192.141.1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 404 Not Found
2022-02-03 22:11:11 erreur 404 : Not Found.
make[1]: *** [Makefile:84: eigen-3.3.7.tar.bz2] Error 8
make[1] : on quitte le répertoire « /home/mboisson/tmp/rvtests-2.1.0/third »
make: *** [Makefile.lib:18: /home/mboisson/tmp/rvtests-2.1.0/third/eigen] Error 2
The above was an attempt to build manually, without any options specified (just make
), which we don't do.
This gist contains the full logs of a build attempted with EasyBuild. It fails to compile nlopt
, I guess because somewhere, somehow, in the mess of the build scripts, it passes wrong arguments. Again, it does NOT need to build nlopt
, we already have it available.
https://gist.github.com/mboisson/fd82f8585f445148eec2dcaedafa090c
It looks like the eigen package cannot be found anymore? Can you modify the script and see if a newer version is available for download? Thank you!
Associate Professor Co-Chair, Bioinformatics and Genomics Graduate Program Dept. Public Health Sciences Institute of Personalized Medicine Penn State College of Medicine, ASB 4301C Email: @.*** URL: https://dajiangliu.blog https://dajiangliu.blog Tel: +1-717-531-4178
On Thu, Feb 3, 2022 at 5:18 PM Maxime Boissonneault < @.***> wrote:
The above was an attempt to build manually, without any options specified (just make), which we don't do.
This gist contains the full logs of a build attempted with EasyBuild. It fails to compile nlopt, I guess because somewhere, somehow, in the mess of the build scripts, it passes wrong arguments. Again, it does NOT need to build nlopt, we already have it available. https://gist.github.com/mboisson/fd82f8585f445148eec2dcaedafa090c
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I would rather not have to download Eigen at all. As I said, we already have it installed.
I pointed our user to the binary version that you have and will forget about building from source. The binary version won't be optimized for our hardware, but I guess it's gonna be good enough.
Hi, I was asked to build this software for our cluster. However, 1) The build procedure does not work 2) We already have all of the third parties
Are there instructions on how to build and install this tool without building all of the vendored dependencies ?