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variani / finemapr

Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF
GNU General Public License v3.0
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Installation issue #8

Open explodecomputer opened 5 years ago

explodecomputer commented 5 years ago

Thanks for making this package. There seems to be an installation issue:

> devtools::install_github("variani/finemapr")
Downloading GitHub repo variani/finemapr@master
Installing 1 packages: cowplot
trying URL 'https://www.stats.bris.ac.uk/R/bin/macosx/el-capitan/contrib/3.6/cowplot_1.0.0.tgz'
Content type 'application/x-gzip' length 1362732 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

The downloaded binary packages are in
    /var/folders/8t/4mzsfqzd5773rsc11w4q5fhw0000gp/T//RtmpLGywNM/downloaded_packages
   checking for file ‘/private/var/folders/8t/4mzsfqzd5773rsc11w4q5fhw0000gp/T/RtmpLGywNM/remotesb21825be3ea7/variani-finemapr-78d5d2f/✔  checking for file ‘/private/var/folders/8t/4mzsfqzd5773rsc11w4q5fhw0000gp/T/RtmpLGywNM/remotesb21825be3ea7/variani-finemapr-78d5d2f/DESCRIPTION’
─  preparing ‘finemapr’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘finemapr/misc’
─  building ‘finemapr_0.1.0.tar.gz’

* installing *source* package ‘finemapr’ ...
** using staged installation
** R
Error in .install_package_code_files(".", instdir) :
files in '/private/var/folders/8t/4mzsfqzd5773rsc11w4q5fhw0000gp/T/Rtmpp7Y6qx/R.INSTALLb48113ddeeda/finemapr/R' missing from 'Collate' field:
  abf.R
  cojo.R
  utils.R
ERROR: unable to collate and parse R files for package ‘finemapr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/finemapr’
Error: Failed to install 'finemapr' from GitHub:
  (converted from warning) installation of package ‘/var/folders/8t/4mzsfqzd5773rsc11w4q5fhw0000gp/T//RtmpLGywNM/fileb2184f88b264/finemapr_0.1.0.tar.gz’ had non-zero exit status

I tried cloning, and document() and install() but still no luck. Any suggestions?

variani commented 5 years ago

The installation should work now.

I'm used to load packages with devtools::load_all() instead of installing + loading, when I actively update the code. I should have add "travis-ci.org" check to keep track installation issues.

explodecomputer commented 5 years ago

Thanks for this @variani

Just to let you know about something - we developed a database of GWAS summary data (https://gwas.mrcieu.ac.uk/) which is what fed into a platform for causal inference testing called MR-Base, it currently has about 25k complete GWAS summary datasets and we're in the process of adding a bunch more. We'll also be making available an API for it soon. This R package https://github.com/MRCIEU/ieugwasr/ is an interface to the API, and we added a function that should conveniently pull down data (ld matrix and gwas summary data) in the format required for finemapr https://github.com/MRCIEU/ieugwasr/blob/master/R/finemapr.R. We're doing this for other packages that use gwas summary data also.

If there's anything that you'd like to see in the ieugwasr package wrt finemapr do let me know

gs115 commented 4 years ago

I am trying to download the updates for Two Sample MR. I used the following code: devtools::install_github("mrcieu/ieugwasr", force=T)

I get this error message Error: Failed to install 'ieugwasr' from GitHub:

What could I do?

explodecomputer commented 4 years ago

Hey @gs115 sorry for the slow reply. It seems to be working ok for me - and travis has the build passing. If the problem persists please post on here https://github.com/mrcieu/ieugwasr/issues with more info e.g. sessionInfo() and full error message