Comments (5)
dajiangliu
commented on June 25, 2024
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
from rvtests.
mboisson
commented on June 25, 2024
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
from rvtests.
mboisson
commented on June 25, 2024
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
from rvtests.
dajiangliu
commented on June 25, 2024
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:
***@***.***>
from rvtests.
mboisson
commented on June 25, 2024
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.
from rvtests.
Related Issues (20)
- User-specified weight per variant
- SKATO: rvtest frozen/stalled (3 variants) (minimal example provided) HOT 1
- What do the duplicated lines in burden test with covariates output mean ?
- What/where is --outputRaw collapsed genotype?
- Reference allele output from rvtest
- Rvtests SKAT,SKATO keeps on running after removing one gene from '--gene' list
- No variants found in gene
- Some permutated p-values >1
- Incorrect phenotype file format [ m2_pheno.pheno ], check column number
- SKAT/CMC: Missing covariates are not imputed, but dropped HOT 2
- Runtime Bug Chromosome 2 UKB WES
- Output MAC or MAF for SKAT-O kernel test
- Output explanation
- Segmentaion fault - rvtests using RStudio Workbench HOT 1
- NAs in assoc file
- Order of Operations when using Frequency filter and Sample exclusion.
- Segmentation fault while running --meta cov
- --setFile how are overlapping regions handled?
- exactCMC N00 is less than N10 and N01 < N11
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from rvtests.