search

PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
4 stars 2 forks source link

Cannot find test.json when compiling Kaphi #106

Closed 0ldM4j0r closed 6 years ago

0ldM4j0r commented 6 years ago

I am getting the following error when trying to compile Kaphi:

* installing to library ‘/home/fabusard/R/x86_64-pc-linux-gnu-library/3.4’
* installing *source* package ‘Kaphi’ ...
** libs
make: Nothing to be done for 'all'.
installing to /home/fabusard/R/x86_64-pc-linux-gnu-library/3.4/Kaphi/libs
** R
** preparing package for lazy loading
Warning in file(con, "r") :
  cannot open file 'test.json': No such file or directory
Error in file(con, "r") : cannot open the connection
Error : unable to load R code in package ‘Kaphi’
ERROR: lazy loading failed for package ‘Kaphi’
* removing ‘/home/fabusard/R/x86_64-pc-linux-gnu-library/3.4/Kaphi’
* restoring previous ‘/home/fabusard/R/x86_64-pc-linux-gnu-library/3.4/Kaphi’
ArtPoon commented 6 years ago

Looks like a leftover text fixture that should either be removed from the test script or added to the repo.

On Sep 11, 2017, at 9:57 AM, Faisal Abu-Sardanah notifications@github.com wrote:

I am getting the following error when trying to compile Kaphi:

  • installing to library ‘/home/fabusard/R/x86_64-pc-linux-gnu-library/3.4 ’

  • installing source package ‘Kaphi’ ... ** libs make: Nothing to be done for 'all' .

installing to /home/fabusard/R/x86_64-pc-linux-gnu-library/3.4/Kaphi/libs R preparing package for lazy loading Warning in file(con, "r") :

cannot open file 'test.json': No such file or directory Error in file(con, "r") : cannot open the connection Error : unable to load R code in package ‘Kaphi ’

ERROR: lazy loading failed for package ‘Kaphi ’

  • removing ‘/home/fabusard/R/x86_64-pc-linux-gnu-library/3.4/Kaphi ’

  • restoring previous ‘/home/fabusard/R/x86_64-pc-linux-gnu-library/3.4/Kaphi’ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

gtng92 commented 6 years ago

I changed the working directory for MASTER simulation output to a folder within Kaphi rather than just on Langley, and I am pushing the changes now.

gtng92 commented 6 years ago

And removed floating test.json call at the bottom of file pkg/R/master-xml-template.R