Installation issue

[explodecomputer]

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]

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]

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]

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]

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