installation

[mebrooks]

While I was troubleshooting my other issue, I started to suspect that the setup never worked (no evidence that save(x, file="x.Rdata") was run at end of a test script). So I tried installing again and I get this error.

checking if libcurl is version 7 and >= 7.22.0... no
configure: error: libcurl >= 7.22.0 library and headers are required with support for https
make[1]: Entering directory `/zhome/61/6/119429/hpc_setup/build'
make[1]: *** No targets specified and no makefile found.  Stop.
make[1]: Leaving directory `/zhome/61/6/119429/hpc_setup/build'

I can also see that my Makevars file is empty.

Any ideas on how to troubleshoot this?

[kaskr]

Are you using the new login host ssh $USER@login2.gbar.dtu.dk ?

https://github.com/DTUAqua/hpc_setup#get-started

[mebrooks]

I was using the old login host login, but I get the same result with the new one. I even tried deleting everything and starting over.

[kaskr]

I get:

n-62-29-1(kaskr) $ curl-config --version
libcurl 7.29.0

And R picks up the right version:

checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.29.0
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.22.0... yes
checking if libcurl supports https... yes

I wonder if you have some old junk in your PATHs ?

[mebrooks]

Yes, it could be the paths. How do I check that?

I get

n-62-29-1(molbr) $ curl-config --version
libcurl 7.63.0

[kaskr]

But wait... Your version is even newer than mine. It makes no sense you get checking if libcurl is version 7 and >= 7.22.0... no You must have been on an old login node when you did the R install. Perhaps try R install again after verifying the new curl version.

[mebrooks]

How do I install R? #1

[mebrooks]

I have this in my .bashrc file

  export PATH=/appl/R/3.5.2-sl64/bin:$PATH

but sometimes I need to use R-3.5.3-mkl2019 because otherwise I got errors when installing packages as below

> install.packages(c("knitr", "rmarkdown", "ggplot2", "bbmle", "plyr"), type="source")
Installing packages into '/zhome/61/6/119429/R/x86_64-pc-linux-gnu-library/3.5'
(as 'lib' is unspecified)
Warning: unable to access index for repository https://mirrors.dotsrc.org/cran/src/contrib:
  internet routines cannot be loaded

> remotes::install_github("mebrooks/selfisher/selfisher")
Error in utils::download.file(url, path, method = download_method(), quiet = quiet,  : 
  internet routines cannot be loaded

Maybe I shouldn't do hpc_setup if it will make it difficult to update packages.

[kaskr]

That's a problem: export PATH=/appl/R/3.5.2-sl64/bin:$PATH no longer needed. Please fix your .bashrc(or whatever) and remove hpc_setup and clone it from scratch. It uses version 3.6.2 which is newer, so no problem with package updates.

[mebrooks]

Should I also delete

module load gcc/6.1.0

?

[kaskr]

Yes

[mebrooks]

I was making a lot of progress with installation. The makefile had a hangup with installing the devtools package and I had to go into R and install a bunch of packages, sometimes looking for errors like

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/zhome/61/6/119429/R/x86_64-pc-linux-gnu-library/3.6/foo/libs/foo.so':
  libR.so: cannot open shared object file: No such file or directory

and then I would install.packages("foo") for whatever foo was in the error message.

After I got devtools installed, I ran MAKE="make -j8" make all again. Then I got stuck at a point where it couldn't install the V8 package. This is the error message

Using PKG_LIBS=-lv8 -lv8_libplatform
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find the libv8 engine library. Try installing:
 * deb: libv8-dev or libnode-dev (Debian / Ubuntu)
 * rpm: v8-devel (Fedora, EPEL)
 * brew: v8 (OSX)
 * csw: libv8_dev (Solaris)
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
---------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:10: fatal error: v8.h: No such file or directory
compilation terminated.
------------------------------------------------------------------------
ERROR: configuration failed for package 'V8'
* removing '/zhome/61/6/119429/R/x86_64-pc-linux-gnu-library/3.6/V8'

I found this related issue, but yum says You need to be root to perform this command.

[mebrooks]

The HPC maintainers installed v8 to solve that problem. Then, I ran MAKE="make -j8" make all again. I went through several of the same rounds as above with messages about .so files and solved them the same as above. I don't know what's wrong with my setup that it wasn't automatically working. Maybe it was because I already had things installed and complied under different settings. Anyhow, in the end I got it to work. It just took time and patience.