SAIGE install fails, multiple methods (Centos 6.x) #166
Comments
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Hi, |
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Greetings!
I am able to retrieve the file in the failed step at any time using wget.
Perhaps the install doesn’t accept system-declared or user-declared proxy server values.
Where can “<long_ID_number>.tar.gz” (or the resulting directory “savvy-<long_ID_number>”) be placed so that this command succeeds?
R CMD INSTALL SAIGE
Is there any file to edit under the git-pulled “SAIGE” directory?
** using staged installation
Downloading https://github.com/statgen/savvy/archive/<long_ID_number>.tar.gz
[----------------------------------------------------------------------] 0%
Download failed with error 400 for: //github.com/statgen/savvy/archive/<long_ID_number>.tar.gz
…-John
From: weizhouUMICH <notifications@github.com>
Sent: Monday, March 23, 2020 6:35 PM
To: weizhouUMICH/SAIGE <SAIGE@noreply.github.com>
Cc: Burns, W. J. <wjb2130@cumc.columbia.edu>; Author <author@noreply.github.com>
Subject: Re: [weizhouUMICH/SAIGE] SAIGE install fails, multiple methods (Centos 6.x) (#166)
Hi,
The error is probably is probably due to some website down for downloading some dependency for savvy, which happened before. If you try again later, you may not see the error.
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Also, if I do the following in R:
httr::set_config(httr::use_proxy("<url_for_proxy_server>",port=8080));
the other method (“devtools::install_github("weizhouUMICH/SAIGE");”) fails for the exact same reason.
It isn’t that savvy/archive/<long_ID_number>.tar.gz is sometimes available, sometimes not. It is *never* available using whatever retrieval method is in your installer. It is always retrievable with wget, or clicking link in Windows. There is some kind of re-direct /aliasing in play.
So if there is some way to tell your installer the savvy archive file is present, or to put a local location instead of the download attempt, this could move forward….
From: Burns, W. J.
Sent: Tuesday, March 24, 2020 4:19 PM
To: weizhouUMICH/SAIGE <reply@reply.github.com>; weizhouUMICH/SAIGE <SAIGE@noreply.github.com>
Cc: Author <author@noreply.github.com>
Subject: RE: [weizhouUMICH/SAIGE] SAIGE install fails, multiple methods (Centos 6.x) (#166)
Greetings!
I am able to retrieve the file in the failed step at any time using wget.
Perhaps the install doesn’t accept system-declared or user-declared proxy server values.
Where can “<long_ID_number>.tar.gz” (or the resulting directory “savvy-<long_ID_number>”) be placed so that this command succeeds?
R CMD INSTALL SAIGE
Is there any file to edit under the git-pulled “SAIGE” directory?
** using staged installation
Downloading https://github.com/statgen/savvy/archive/<long_ID_number>.tar.gz<https://github.com/statgen/savvy/archive/%3clong_ID_number%3e.tar.gz>
[----------------------------------------------------------------------] 0%
Download failed with error 400 for: //github.com/statgen/savvy/archive/<long_ID_number>.tar.gz
…-John
From: weizhouUMICH <notifications@github.com<mailto:notifications@github.com>>
Sent: Monday, March 23, 2020 6:35 PM
To: weizhouUMICH/SAIGE <SAIGE@noreply.github.com<mailto:SAIGE@noreply.github.com>>
Cc: Burns, W. J. <wjb2130@cumc.columbia.edu<mailto:wjb2130@cumc.columbia.edu>>; Author <author@noreply.github.com<mailto:author@noreply.github.com>>
Subject: Re: [weizhouUMICH/SAIGE] SAIGE install fails, multiple methods (Centos 6.x) (#166)
Hi,
The error is probably is probably due to some website down for downloading some dependency for savvy, which happened before. If you try again later, you may not see the error.
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Hi @jonathonl |
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I have not seen this error before. It seems a little odd that the error message prints |
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cget, version 0.1.8
Same error, “Download failed with error 400 for: //github.com/statgen/savvy/archive/5cf549634d535c07f08af4e52de67ecbf960d78e.tar.gz”
If I try to install the wget-retrieved file directly (cget install 5cf549634d535c07f08af4e52de67ecbf960d78e.tar.gz) I get:
Download failed with error 400 for: //github.com/jonathonl/shrinkwrap/archive/v1.0.0-beta.tar.gz
Failed to build package 5cf549634d535c07f08af4e52de67ecbf960d78e.tar.gz
From: Jonathon LeFaive <notifications@github.com>
Sent: Wednesday, March 25, 2020 12:07 PM
To: weizhouUMICH/SAIGE <SAIGE@noreply.github.com>
Cc: Burns, W. J. <wjb2130@cumc.columbia.edu>; Mention <mention@noreply.github.com>
Subject: Re: [weizhouUMICH/SAIGE] SAIGE install fails, multiple methods (Centos 6.x) (#166)
I have not seen this error before. It seems a little odd that the error message prints //github.com/... and not https://github.com/. @jbsysadmin<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jbsysadmin&d=DwMCaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=pta2tZv18oq3RBvnU7cWROhNVXtf6jawEznUq0BcNwg&s=DBbxySfYW9lehE6MPEhBxrp3kqP-6QreGnFciUoz258&e=>, what version of cget do you have (cget --version)? Do you get the same error when you run cget install statgen/savvy@5cf5496?
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Hmm... can you run |
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I just spun up a Centos 6 VM and was able to use cget to install savvy without receiving that error. Do you have pip3 installed? If so, I would try uninstalling cget and then installing with pip3 instead? Since Centos 6 is pretty old, you may run into other issues as well. You'll need a g++ version >= v5.0 and cmake >= 3.2. The default centos 6 packages do not meet these requirements. |
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The pip I uses in in Python 3.8.1. Any dependencies listed on your site (cmake/ gcc) are answered in custom compiles of later versions.
Re-installing with pip3 made no difference.
Was your VM behind a proxy? Do you know of any cget accommodation for that?
From: Jonathon LeFaive <notifications@github.com>
Sent: Wednesday, March 25, 2020 2:37 PM
To: weizhouUMICH/SAIGE <SAIGE@noreply.github.com>
Cc: Burns, W. J. <wjb2130@cumc.columbia.edu>; Mention <mention@noreply.github.com>
Subject: Re: [weizhouUMICH/SAIGE] SAIGE install fails, multiple methods (Centos 6.x) (#166)
I just spun up a Centos 6 VM and was able to use cget to install savvy without receiving that error. Do you have pip3 installed? If so, I would try uninstalling cget and then installing with pip3 instead?
Since Centos 6 is pretty old, you may run into other issues as well. You'll need a g++ version >= v5.0 and cmake >= 3.2. The default centos 6 packages do not meet these requirements.
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You are receiving this because you were mentioned.
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If your web traffic is being proxied, then that could very well be the problem you could try adding the --insecure flag to Alternatively, you could install dependencies manually, but there are multiple layers of dependencies so this approach is quite involved. Another option would be to build a SAIGE binary package ( |
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I tried “—insecure” earlier today, but forgot to mention.
Thanks for the suggestions,
-John
You wrote:
If your web traffic is being proxied, then that could very well be the problem you could try adding the --insecure flag to cget install in hopes that http behaves better than https (see pfultz2/cget#52<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pfultz2_cget_issues_52&d=DwMCaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=Lcm_WqJ_rUVrU3IQt7ALp57NrOU09lZVgNzJYrKHguE&m=ml9eMMIJdoYbtC0avFV89ZRhyvCVMjujI2R92fNVPR0&s=Nq_dF_CyazAqD69nPb4wBhALg7f9a7GUd4AyoyCsXjw&e=>).
Alternatively, you could install dependencies manually, but there are multiple layers of dependencies so this approach is quite involved.
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You could try working with the cget maintainer to get this resolved (pfultz2/cget#52). Otherwise, these are the dependencies that would need to be manually installed: You would then need to modify the configure script in SAIGE to not run cget. |
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We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ Thanks! |
Greetings.
The install method below fails with the output shown at bottom. gcc 8.2, R 3.6.3. Any leads?
"devtools::install_github("weizhouUMICH/SAIGE"" did not work either.
Centos 6.10
Method:
git clone --depth 1 -b master https://github.com/weizhouUMICH/SAIGE
R CMD INSTALL SAIGE
Output:
** using staged installation
Downloading https://github.com/statgen/savvy/archive/5cf549634d535c07f08af4e52de67ecbf960d78e.tar.gz
[----------------------------------------------------------------------] 0%
Download failed with error 400 for: //github.com/statgen/savvy/archive/5cf549634d535c07f08af4e52de67ecbf960d78e.tar.gz
Failed to build package statgen/savvy
Waf: The wscript in '/usr/local/installs/saige/SAIGE/thirdParty/bgen' is unreadable
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