R 3.6: libRlapack.so: cannot open shared object file: No such file or directory

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1

Hi,

Since a few days, we do have some problems with R 3.6 and libRlapack.so in travis-ci.

Our config looks like the following:

# TravisCI container
os: linux
dist: xenial
warnings_are_errors: false

# R environment, dependencies and information
language: r
r:
  - 3.3
  - 3.4
  - 3.5
  - 3.6
cache: packages
repos:
  CRAN: https://cloud.r-project.org

# Installation
install:
    # package dependencies
    - sudo apt-get install libudunits2-dev
    # package installation
    - Rscript install.R

# Tests
script:
    - Rscript tests.R

Within our local script install.R, we install the igraph package via install.packages("igraph", dependencies = TRUE, verbose = FALSE, quiet = FALSE)

This has worked for all the requested R versions (3.3, 3.4, 3.5, and 3.6) until August 26, 2020. However, since September 02, 2020, this does not work any more for R 3.6 (3.3 to 3.5 still work as before), resulting in the following error during installation, as you can see in the following excerpt from the log file:

$ Rscript -e 'sessionInfo()'
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.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_3.6.3
$ sudo apt-get install libudunits2-dev
$ Rscript install.R
$ Rscript tests.R
Loading required namespace: igraph
Failed with error:  ‘unable to load shared object '/home/travis/R/Library/igraph/libs/igraph.so':
  libRlapack.so: cannot open shared object file: No such file or directory’

Does someone know why this does fail now? It only fails for R 3.6, not for previous R versions, and also it did not fail for R 3.6 until the end of August…

Best,
Thomas

2

I have the same problem (see Travis CI error log) on R-devel and Xenial.

I noticed something special in a Travis CI log:

$ Rscript -e 'sessionInfo()'
R Under development (unstable) (2020-10-09 r79317)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so <--- HERE

Maybe that will help @jeroen and @jimhester to fix it?

3

Try wiping or removing your cache.

4

Indeed, wiping the cache is the solution! Thanks @jeroen!