traviz 1.0.0 installation fails: ERROR: lazy loading failed
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@1058197c
Last seen 4 days ago
United States

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source).

I have a conda environment, and I installed traviz from conda, but it cannot be used - when I do library(traviz) R just crashes and quits without any message. So I tried to install it using BiocManager::install(). But it fails - please see below. I also tried from command line with R CMD INSTALL with the downloaded tarball, with no luck (same error.)

I could install it on my mac laptop (where R version is 4.1.1, bioconductor 3.14), where it installed from precompiled binaries I believe ... But I need it for large datasets, to work on a linux machine.

Thank you.


> BiocManager::install('traviz', force=T)
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'traviz'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/traviz_1.0.0.tar.gz'
Content type 'application/x-gzip' length 3228371 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

* installing *source* package ‘traviz’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package ‘traviz’
* removing ‘/<somedir>/env3/lib/R/library/traviz’
* restoring previous ‘/<somedir>/env3/lib/R/library/traviz’

The downloaded source packages are in
        ‘/tmp/RtmpBSPxPc/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'AnnotationDbi', 'BiocParallel', 'fansi', 'GenomicRanges',
  'HDF5Array', 'httpuv', 'igraph', 'later', 'metap', 'NMF', 'RcppParallel',
  'RSQLite', 'S4Vectors', 'scran', 'xgboost'
Update all/some/none? [a/s/n]: n
Warning message:
In .inet_warning(msg) :
  installation of package ‘traviz’ had non-zero exit status

sessionInfo( )

R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /<somedir>/env3/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.1.2
traviz • 91 views
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I think I figured this out. I could fix it by (re)installing rgl (rgl_0.108.3) package from within R (install.packages('rgl')). After that both conda version of traviz as well as one using BiocManager::install('traviz') work. The issue seems to be in the conda version of the rgl (r-rgl) which it installed as a pre-requisite.

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Entering edit mode
@1058197c
Last seen 4 days ago
United States

Replacing conda's installation of the pre-requisite r-rgl (0.108.3) with manual install within R (install.packages('rgl')) solves the issue for traviz.

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