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Bioconductor / bioconductor_docker

Docker Containers for Bioconductor
https://bioconductor.org/help/docker/
Artistic License 2.0
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EBImage failing in 3.20 #112

Open almahmoud opened 2 weeks ago

almahmoud commented 2 weeks ago

EBImage is failing in 3.20 with

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/local/lib/R/site-library/tiff/libs/tiff.so':
  libtiff.so.5: cannot open shared object file: No such file or directory

Likely due to missing sysdep, but noting here to look into it later

almahmoud commented 2 weeks ago

ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.6 /usr/lib/x86_64-linux-gnu/libtiff.so.5 seems to bypass the issue. Uninstalling libtiff6-dev and only installing libtiff5-dev doesn't work, libtiff5-dev seems to always come with libtiff6. Haven't looked too much into it though

vjcitn commented 2 weeks ago

Within the 3.20 container, I got EBImage to install by installing the CRAN source package for tiff with R CMD INSTALL prior to BiocManager::install("EBImage")

wget https://cran.r-project.org/src/contrib/tiff_0.1-12.tar.gz
R CMD INSTALL tiff_0.1-12.tar.gz
# now in R use BiocManager::install("EBImage")
almahmoud commented 2 weeks ago

Good catch... I think the issue is that it's trying to use a wrong binary