Problems with bioconductor after updating R to 3.6.2
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crgarcia • 0
@crgarcia-22590
Last seen 16 months ago

Hi, I just updated R to latest version 3.6.2 and I can not longer install phyloseq. I get a message of error for packages igraph and phangorn.

Code:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.10")

Errors:

##########for igraph
installing to /usr/local/lib/R/site-library/00LOCK-igraph/00new/igraph/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/00LOCK-igraph/00new/igraph/libs/igraph.so':
  libgfortran.so.4: no se puede abrir el archivo del objeto compartido: No existe el archivo o el directorio
Error: loading failed
and phangorn
installing to /usr/local/lib/R/site-library/00LOCK-phangorn/00new/phangorn/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘igraph’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Ejecución interrumpida
ERROR: lazy loading failed for package ‘phangorn’
* removing ‘/usr/local/lib/R/site-library/phangorn’
* restoring previous ‘/usr/local/lib/R/site-library/phangorn’

The downloaded source packages are in
    ‘/tmp/RtmpZVhmlz/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘igraph’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘phangorn’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘igraph’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘phangorn’ had non-zero exit status
R 3.6.2 update problems with igraph and phangorn update Phyloseq igraph phangorn Tutorial • 741 views
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What is your sessionInfo( ) ? Depending this thread might be of interest https://github.com/igraph/rigraph/issues/275

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Some output is missing from your attempt to install igraph. I see

> BiocManager::install("igraph")
Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable)
  (2019-12-20 r77608)
Installing package(s) 'igraph'
trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.2.4.2.tar.gz'
Content type 'application/x-gzip' length 2712085 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
...

are you using conda or something?

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