Can't install package oligoClasses
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salamandra • 0
@salamandra-12825
Last seen 8 months ago

When I try to install oligoClasses on rstudio:

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

BiocManager::install("oligoClasses")


gives error:

Error: objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff'
Execution halted
* removing ‘/home/tania/anaconda3/envs/r_3.6/lib/R/library/oligoClasses’
* restoring previous ‘/home/tania/anaconda3/envs/r_3.6/lib/R/library/oligoClasses’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
installation of package ‘oligoClasses’ had non-zero exit status


Then I tried:

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


which is suggested here, but keeps giving same error when installing oligoClasses

library(oligoClasses)


gives:

Error: package or namespace load failed for ‘oligoClasses’:
objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff'


I am running rstudio from within a conda env with R 3.6.1 installed on a ubuntu computer.

R oligoClasses ff • 1.5k views
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@kevin
Last seen 1 hour ago

As you imply that you are using Conda, can you instead try (outside R):

conda install -c bioconda bioconductor-oligoclasses


Kevin

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Hopefully that works. I don't use Conda (for R/BioC at least), so I don't know how up-to-date they keep things.

This error was due to a breaking change in what the ff package exports, that Rob Scharpf and I fixed in early August. The OP needs oligoClasses 1.50.4 if using release and 1.51.4 if using devel.

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actually is not working...

library(oligoClasses)
Error: package or namespace load failed for ‘oligoClasses’:
objects ‘open.ff’, ‘close.ff’ are not exported by 'namespace:ff'

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Well, I don't know how Conda works in the context of R and Bioconductor, so it might be a horrible idea to install directly, but you might try

library(BiocManager)
install("oligoClasses")


Which should get you the updated version of oligoClasses that has the fix.

I use Conda for Python, because Python is so stupidly picky about like everything, plus the fact that so much code relies on Python 2.7 instead of being updated to living in 2020 and using Python 3. But I digress.

Anyway, I don't see a compelling reason to use Conda for R, which is really easy to install (even on a Linux box where you might not have sudo privileges - I've been running my own R versions on Linux for years now). So if the above doesn't work or is a horrible idea, you might consider just using a regular installation, which IMO is preferable.

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Oh. Wait a minute. You are using R-3.6.1? That's not gonna work. You need R-4.0.0 at minimum, and a re-installation of Bioconductor. Since ff is a CRAN package, you get the current version, which has changed what functions are exported. The changes that Rob and I made are only in effect for the release and devel versions of Bioconductor, both of which rely on R-4.0.0 or higher (e.g, you could use R-4.0.1 or R-4.0.2, but not anything prior).

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Had to install R4 without anaconda. thanks!