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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
160 stars 87 forks source link

R installation broken #52

Closed mheskett closed 5 years ago

mheskett commented 5 years ago

Using R=3.6.

If set up correctly your R recipe should find these dependencies and install them automatically. Also, the commit "--no-docs" is not found, so that is out of date.

install_github("broadinstitute/ichorCNA") Downloading GitHub repo broadinstitute/ichorCNA@master Skipping 4 packages not available: HMMcopy, plyr, GenomicRanges, GenomeInfoDb ✔ checking for file ‘/tmp/Rtmp84DLC0/remotes3f0b339a480c/broadinstitute-ichorCNA-b32b215/DESCRIPTION’ (1.1s) ─ preparing ‘ichorCNA’: ✔ checking DESCRIPTION meta-information ... Warning: /tmp/Rtmpkp4yri/Rbuild807073702cc6/ichorCNA/man/ichorCNA-package.Rd:21: unexpected section header '\author' Warning: /tmp/Rtmpkp4yri/Rbuild807073702cc6/ichorCNA/man/ichorCNA-package.Rd:27: unexpected section header '\examples' Warning: /tmp/Rtmpkp4yri/Rbuild807073702cc6/ichorCNA/man/ichorCNA-package.Rd:35: unexpected END_OF_INPUT ' ' ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories Removed empty directory ‘ichorCNA/scripts’ ─ building ‘ichorCNA_0.3.0.tar.gz’

ERROR: dependencies ‘HMMcopy’, ‘plyr’, ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘ichorCNA’

gavinha commented 5 years ago

Hi @mheskett

Both https://cloud.r-project.org and https://cran.r-project.org/ are unresponsive for me. Perhaps wait until their servers are accessible. Installing dependencies is something that install_github handles and it seems by default it looks there.

Under Installation, you can also try Option 2.

Hope this helps.

jgarces02 commented 5 years ago

Hi @gavinha,

I had a similar error:

Downloading GitHub repo broadinstitute/ichorCNA@master
√  checking for file 'C:\Users\jgarces\AppData\Local\Temp\RtmpMZJYTL\remotes4cec46ebd94\broadinstitute-ichorCNA-d91730c/DESCRIPTION' ... 
-  preparing 'ichorCNA':
√  checking DESCRIPTION meta-information ... 
   Warning: C:/Users/jgarces/AppData/Local/Temp/RtmpS4ApYg/Rbuild13cc598b6e99/ichorCNA/man/ichorCNA-package.Rd:21: unexpected section header '\author'
   Warning: C:/Users/jgarces/AppData/Local/Temp/RtmpS4ApYg/Rbuild13cc598b6e99/ichorCNA/man/ichorCNA-package.Rd:27: unexpected section header '\examples'
   Warning: C:/Users/jgarces/AppData/Local/Temp/RtmpS4ApYg/Rbuild13cc598b6e99/ichorCNA/man/ichorCNA-package.Rd:35: unexpected END_OF_INPUT '
   '
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
   Removed empty directory 'ichorCNA/scripts'
-  building 'ichorCNA_0.3.0.tar.gz'

Installing package into ‘C:/Users/jgarces/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package 'ichorCNA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Error : (convertido del aviso) C:/Users/jgarces/AppData/Local/Temp/RtmpqICA2T/R.INSTALL4f6c230d5f02/ichorCNA/man/ichorCNA-package.Rd:21: unexpected section header '\author'
ERROR: installing Rd objects failed for package 'ichorCNA'
* removing 'C:/Users/jgarces/Documents/R/win-library/3.6/ichorCNA'
Error: Failed to install 'ichorCNA' from GitHub:
  (converted from warning) installation of package ‘C:/Users/jgarces/AppData/Local/Temp/RtmpMZJYTL/file4cec3d7a78d5/ichorCNA_0.3.0.tar.gz’ had non-zero exit status

And I've also tried to clone the github repository with problems too... any idea, please? Thanks!

Cloning into 'ichorCNA'...
The authenticity of host 'github.com (140.82.118.3)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
Are you sure you want to continue connecting (yes/no)? y
Please type 'yes' or 'no': yes
Warning: Permanently added 'github.com,140.82.118.3' (RSA) to the list of known hosts.
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
mheskett commented 5 years ago

I can confirm R-CRAN is responsive and get this error


✔  checking for file ‘/tmp/RtmpjE9Oie/remotes154595ac465af/broadinstitute-ichorCNA-d91730c/DESCRIPTION’ (1.6s)
─  preparing ‘ichorCNA’:
✔  checking DESCRIPTION meta-information ...
   Warning: /tmp/RtmpdhRv0G/Rbuild18e885b9e3082/ichorCNA/man/ichorCNA-package.Rd:21: unexpected section header '\author'
   Warning: /tmp/RtmpdhRv0G/Rbuild18e885b9e3082/ichorCNA/man/ichorCNA-package.Rd:27: unexpected section header '\examples'
   Warning: /tmp/RtmpdhRv0G/Rbuild18e885b9e3082/ichorCNA/man/ichorCNA-package.Rd:35: unexpected END_OF_INPUT '
   '
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘ichorCNA/scripts’
─  building ‘ichorCNA_0.3.0.tar.gz’

* installing *source* package ‘ichorCNA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Error : (converted from warning) /tmp/Rtmp9Uo7M9/R.INSTALL18f3d1b76e86/ichorCNA/man/ichorCNA-package.Rd:21: unexpected section header '\author'
ERROR: installing Rd objects failed for package ‘ichorCNA’
* removing ‘/home/groups/Spellmandata/heskett/packages/envs/test123/lib/R/library/ichorCNA’
Error: Failed to install 'ichorCNA' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpjE9Oie/file15459101e3fe9/ichorCNA_0.3.0.tar.gz’ had non-zero exit status```
jgarces02 commented 5 years ago

Perfect. If CRAN is the responsible, I guess installing it from Github would be possible but I've also problems... maybe I'm doing something wrong. Thanks again for your help!

gavinha commented 5 years ago

Hi @mheskett

Please let me know if you are still having issues with the installation after the small change in the last commit.

Thanks, Gavin

jgarces02 commented 5 years ago

Solved! Thank you so much!