CODEWITHSUNDEEP
rubuntuubuntu-18.04forecast
Blairg23
Blairg23

Reputation: 12065

Errors during installation of R dependencies after new R installation on Ubuntu 18.04

System: Ubuntu 18.04

Original error that showed up that prompted me to try to reinstall R and dependencies:

Error: package or namespace load failed for 'lubridate' in dyn.load(file, DLLpath = DLLpath, ...):  unable to load shared object '/usr/local/lib/R/site-library/stringi/libs/stringi.so':   libicui18n.so.57: cannot open shared object file: No such file or directory

Steps to reproduce:

  1. Install R: apt install r-base
  2. Try to install R dependencies: install.packages(c("dplyr", "lubridate", "qcc", "forecast"), repos='http://cran.us.r-project.org')

Error that displays during installation:

/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated

Error that displays after installation:

The downloaded source packages are in
    '/tmp/RtmpnulsEe/downloaded_packages'
Warning message:
In install.packages(c("dplyr", "lubridate", "qcc", "forecast", "stringi"),  :
  installation of package 'forecast' had non-zero exit status

After purging and reinstalling r-base and R dependencies, I'm seeing this...(already checked that libcurl4-openssl-dev was latest version):

Error: package or namespace load failed for 'forecast' in dyn.load(file, DLLpath = DLLpath, ...): 
unable to load shared object '/usr/local/lib/R/site-library/curl/libs/curl.so':
/usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /usr/local/lib/R/site-library/curl/libs/curl.so)

Update: Apparently it's something in the forecast library, because I reproduced that error like this:

$ R
> library(forecast)
Error: package or namespace load failed for 'forecast' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/curl/libs/curl.so':
  /usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /usr/local/lib/R/site-library/curl/libs/curl.so)

Upvotes: 2

Views: 2115

Answers (2)

Blairg23
Blairg23

Reputation: 12065

After trying the following (purging and reinstalling R between each step):

  1. apt purge r-base
  2. Added/removed several different PPAs before realizing none of them supported Bionic Beaver. Result: Release not found.
  3. Found Michael Rutter's PPA and attempted to use that. Result: same error message from above ('CURL_OPENSSL_3' not found).
  4. Attempting several solutions to this SO article. Result: same error message from above ('CURL_OPENSSL_3' not found).

  5. Read this article and performed the following in R:

    > remove.packages("curl")
> install.packages("curl")
> install.packages(c("dplyr", "lubridate", "qcc", "forecast", "stringi", "curl"), repos='http://cran.us.r-project.org')

And everything worked as intended.

Upvotes: 1

Dirk is no longer here
Dirk is no longer here

Reputation: 368231

Your original problem is that stringi was built against a distro package version of libicu which changed. As this distribution package does not know you have lubridate in /usr/local it changes and breaks things.

There are a number of ways to fix this. The easiest (and narrowest) is to make sure you have libicu-dev installed. You could then reinstall (ie: rebuild stringi) after which lubridate will load.

For the rest you are just going somewhat wild throwing everything that is moveable up against the wall. You need to take a moment to realize that you can either install all these as binaries (ie from the Michael Rutter PPAs at launchpad), or from source. Your call. I have an older answer explaining the difference here (as well as in other follow-ups here) and we help on the r-sig-debian list too.

But in short: read this README at CRAN (esp first few paragraphs) and consider the PPAs.

Upvotes: 3

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