installation issue with ubuntu 20.04

[vjbaskar]

I am trying to install cistopic in ubuntu:20.04 and it looks like cisTopic needs libgfortran3 which is no longer supported by it now. The least apt supports is libgfortran4. Am I missing something here, that would solve this issue quickly?
Thanks!
Vijay

[cbravo93]

Hi @vjbaskar !

Could you paste the exact error you are getting (the whole output when you are trying to install it).

Thanks!

[vjbaskar]

Hi @cbravo93,

It is part of my docker container that I run using Singularity in our HPC. It installs fine, no problem there. When I load the library it gives the error below.

Error: package or namespace load failed for ‘cisTopic’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/library/float/libs/float.so':
  libgfortran.so.3: cannot open shared object file: No such file or directory
Traceback:

1. library(cisTopic)
2. tryCatch({
 .     attr(package, "LibPath") <- which.lib.loc
 .     ns <- loadNamespace(package, lib.loc)
 .     env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
 . }, error = function(e) {
 .     P <- if (!is.null(cc <- conditionCall(e))) 
 .         paste(" in", deparse(cc)[1L])
 .     else ""
 .     msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
 .         sQuote(package), P, conditionMessage(e))
 .     if (logical.return) 
 .         message(paste("Error:", msg), domain = NA)
 .     else stop(msg, call. = FALSE, domain = NA)
 . })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop(msg, call. = FALSE, domain = NA)

So when print its shared lib dependencies, I get this

Singularity> ldd /usr/local/lib/R/library/float/libs/float.so
	linux-vdso.so.1 (0x00007ffea67ea000)
	libRlapack.so => /usr/local/lib/R/lib/libRlapack.so (0x00002ac831a37000)
	libRblas.so => /usr/local/lib/R/lib/libRblas.so (0x00002ac831c27000)
	libgfortran.so.3 => not found
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002ac831c5d000)
	libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002ac831dac000)
	libR.so => /usr/local/lib/R/lib/libR.so (0x00002ac831df6000)
	libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00002ac8322a8000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00002ac8322ea000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002ac83230d000)
	libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x00002ac8324ff000)
	/lib64/ld-linux-x86-64.so.2 (0x00002ac831847000)
	libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8 (0x00002ac8327c7000)
	libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00002ac832817000)
	liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00002ac8328a9000)
	libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00002ac8328d2000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00002ac8328e5000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002ac832901000)
	libicuuc.so.66 => /lib/x86_64-linux-gnu/libicuuc.so.66 (0x00002ac832907000)
	libicui18n.so.66 => /lib/x86_64-linux-gnu/libicui18n.so.66 (0x00002ac832aed000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002ac832dee000)
	libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6 (0x00002ac832e09000)
	libicudata.so.66 => /lib/x86_64-linux-gnu/libicudata.so.66 (0x00002ac832e39000)
	libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00002ac8348fa000)

This may as well be an error due to containerisation + singularity + R combination but I have no way of testing this independently elsewhere.

Many thanks
Vijay

[cbravo93]

Hi!

Can you check if you actually have gfortran in your image (locate gfortran)?

Normally I work with a conda R environment in HPC, that does not give issues so far.

Cheers!

C