unable to install bioconductor package

Hello everybody. Please, give me suggestions. I tried to install on Ubuntu 18 package "OligoClasses" from Bioconductor but it gives the following error: " Error: objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff' " despite package "ff" is correctly installed (see the end of the code).

BiocManager::install("oligoClasses")

  • installing source package ‘oligoClasses’ ...
    ** using staged installation
    ** R
    ** data
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error: objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff'
    Execution halted
    ERROR: lazy loading failed for package ‘oligoClasses’
  • removing ‘/home/odysseus/R/x86_64-pc-linux-gnu-library/4.0/oligoClasses’

The downloaded source packages are in
‘/tmp/Rtmpbp8RWG/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘oligoClasses’ had non-zero exit status

Therefore I tried to build it from source and the to install it, but result was the same:

sudo R CMD build oligoClasses

  • checking for file ‘oligoClasses/DESCRIPTION’ ... OK
  • preparing ‘oligoClasses’:
  • checking DESCRIPTION meta-information ... OK
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
  • looking to see if a ‘data/datalist’ file should be added
  • building ‘oligoClasses_1.50.0.tar.gz’

sudo R CMD INSTALL oligoClasses_1.50.0.tar.gz

  • installing to library ‘/home/odysseus/R/x86_64-pc-linux-gnu-library/4.0’
  • installing source package ‘oligoClasses’ ...
    ** using staged installation
    ** R
    ** data
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error: objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff'
    Execution halted
    ERROR: lazy loading failed for package ‘oligoClasses’
  • removing ‘/home/odysseus/R/x86_64-pc-linux-gnu-library/4.0/oligoClasses’

Correct installation of package "ff":

installing to /home/odysseus/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-ff/00new/ff/libs
** R
** exec
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

  • DONE (ff)

Any suggestion, please?
Thanks in advance,
Alberto

1 Like

It seems there's a recent update of ff package (dependency of OligoClassees; ArrayExpress as well), causing this issue. Just updated at 2020-07-30 for the latest version 2.2.14.2 (https://cran.r-project.org/web/packages/ff/index.html).
Previous version that works is 2.2.14. Directly use this URL to re-install this package and restart Rstudio:

install.packages('https://cran.r-project.org/src/contrib/Archive/ff/ff_2.2-14.tar.gz',repos=NULL)

3 Likes

Thanks a lot, Herdiants. It worked perfectly

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