Installing densvis on a Singularity container
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

When installing densvis on a Singularity container, it seems to ignore the g++ that comes with the container, and instead is finding the site-wide g++ even though it doesn't have access to that version of g++, nor even access to the directory structure that contains the site-wide g++ (g++ is installed as a module on this linux box, and I haven't loaded that module prior to starting the singularity container, so technically it shouldn't be able to find it at all).

> library(BiocManager)
> install("densvis")
<snip>
* installing *source* package ‘densvis’ ...
** using non-staged installation via StagedInstall field
** libs
/share/apps/GCC/gcc-10.3.0/bin/g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -O3 -march=native -mtune=native -fPIC -c RcppExports.cpp -o RcppExports.o
/bin/bash: /share/apps/GCC/gcc-10.3.0/bin/g++: No such file or directory
make: *** [/usr/local/lib/R/etc/Makeconf:177: RcppExports.o] Error 127
ERROR: compilation failed for package ‘densvis’
* removing ‘/usr/local/lib/R/host-site-library/densvis’

## However
> system("which g++")
/usr/bin/g++

> file.exists("/share/")
[1] FALSE

It appears to use basilisk::configureBasiliskEnv to get some environment variables, but it's not clear to me if that is the issue or not.

densvis docker • 2.0k views
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got the same issue, have you solved it?

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The question is not reproducible as it is unclear which base image you're talking about. I can install as above from source in the latest rocker/rstudio bootstrapped from Docker. Do you install directly from a Singularity file or how was the image even built?

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I don't currently have access to a HPC with a module system so it'll be a while before I can debug this. Does Aaron Lun have any insights from the basilisk side of things?

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@james-w-macdonald-5106
Last seen 1 hour ago
United States

Most (I thought all?) packages for Singularity and Docker instances should be binaries, which eliminates the issue.

> install("densvis")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'densvis'
trying URL 'https://bioconductor.org/packages/3.17/container-binaries/bioconductor_docker/src/contrib/densvis_1.10.1_R_x86_64-pc-linux-gnu.tar.gz'
Content type 'application/gzip' length 2301194 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *binary* package 'densvis' ...
* DONE (densvis)

It took a while for the binaries to get built, but it appears most are available now.

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I tried BioMnager::install, but got an error "Error 1 ERROR; compilation failed for package 'densvis'". I am using a mac. BiocManager::installerror in compilation

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I get the same error when I try to install densvis in R with BiocManager::install("densvis") and I have no idea how to solve this problem. I also tried with install("densvis") only, but same error occurred.

Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)

Could someone please tell me how to fix this? `

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Do you have gfortran installed? eg this installation package

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