Instructions to build without all of the third parties ?

[mboisson]

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 ?

[dajiangliu]

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, 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 ? — Reply to this email directly, view it on GitHub <#136>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNCDJIT5RNPTO62UUZTKNLUZLTAJANCNFSM5NP77ZBA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- All the best, Dajiang -- 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

[mboisson]

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

[mboisson]

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

[dajiangliu]

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! All the best, Dajiang -- 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 — Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNCDJKX5RGBK37L2HCNB4TUZL5JNANCNFSM5NP77ZBA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[mboisson]

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.