pati-ni
commented
12 months ago Sorry for the delayed response, but it looks like there might be a problem with your R setup. Can you install other packages using CRAN and/or github?
Closed Citugulia40 closed 9 months ago
pati-ni
commented
12 months ago Sorry for the delayed response, but it looks like there might be a problem with your R setup. Can you install other packages using CRAN and/or github?
michellemeier27
commented
10 months ago I have the same issue. I am recomputing an R environment (renv v 1.0.3), so I've been installing packages from github and CRAN all afternoon and this suddenly happened. I am on R-4.3.2 and trying to install harmony v 1.1.0 though.
pati-ni
commented
10 months ago Hi @michellemeier27,
please post full installation log and your sessionInfo().
michellemeier27
commented
10 months ago Hi @pati-ni
I'm going to try and give you all the information I have, but please let me know if there is anything else you need.
I'm attaching the build.log which is the output of R -e 'renv::restore(); install.packages("harmony")' 2>&1 | tee build.log. Then I have a README.md file that I used to store notes when I was generating the r environment, it also contains the modules I load on our cluster (gcc version etc) and the contents of my Makevars.The sessioninfo.log contains sessionInfo() and I'm attaching my renv_lock.log which contains all the versions of the packages that I've downloaded.
pati-ni
commented
10 months ago Thanks for sharing such a detailed overview of your environment.
I see that your workflow is rather complicated. I would start simple by reproducing a minimum failing example. For example, try to only module load R/4.3.2.Core and then try to install harmony. I would also check that there is no other R in the path already...
EDIT: avoid to set the C++ flags. Remove any Makevars files interfering with these
michellemeier27
commented
10 months ago Hi @pati-ni
So I tried installing harmony without my Makevars and only running module load R/4.3.2.Core but still within my r environment which unfortunately still fails. However, if I move outside of my environment it installs without issues. It must be something in the environment that's bothering it during installation. So doesn't seem to be related to harmony itself :) If you have any ideas what it could be clashing with let me know, but I understand that this is not related to your package anymore. My guess is that it might fail because I used my Makevars file to compile packages harmony needs for installation like Rcpp. If I get time this week I will try and recompute everything again without a Makevars file to see if that fixes the issue and update here.
pati-ni
commented
10 months ago It is a wild guess but judging from the messages you are getting I would expect to link your compiler to different library of armadillo compared to what R is loading. Some further investigation of R system-wide Makevars, linked libraries and LD_LIBRARY_PATH and LIBRARY_PATH environment cars could help with this.
Please post here if you get a resolution
On Mon, Nov 20, 2023, 19:27 michellemeier27 @.***> wrote:
Hi @pati-ni https://github.com/pati-ni So I tried installing harmony without my Makevars and only running module load R/4.3.2.Core but still within my r environment which unfortunately still fails. However, if I move outside of my environment it installs without issues. It must be something in the environment that's bothering it during installation. So doesn't seem to be related to harmony itself :) If you have any ideas what it could be clashing with let me know, but I understand that this is not related to your package anymore. My guess is that it might fail because I used my Makevars file to compile packages harmony needs for installation like Rcpp. If I get time this week I will try and recompute everything again without a Makevars file to see if that fixes the issue and update here.
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Hi, I am facing error in installing harmony with R-4.1 version. I have tried to install from CRAN and as well as github.
Please help.
Thanks in advance