Re: [Bioc-devel] VariantAnnotation Installation Compile Error

2021-05-24 Thread Dario Strbenac
Good day, I also see NULL on R start-up. I installed R from source. $ R-4.1.0/bin/R R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" ...... Type 'q()' to quit R. NULL > I noticed a couple of error messages at the end of the installation which I thought were harmless. I will

Re: [Bioc-devel] VariantAnnotation Installation Compile Error

2021-05-24 Thread Vincent Carey
On Sun, May 23, 2021 at 10:00 PM Dario Strbenac wrote: > Good day, > > I apparently have a valid Bioconductor package library but > VariantAnnotation won't install successfully. > > > valid() > [1] TRUE > > install("VariantAnnotation") > Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2

Re: [Bioc-devel] VariantAnnotation Installation Compile Error

2021-05-24 Thread Dario Strbenac
Good day, No, the temporary directory has space remaining. I wonder what file it is referring to by "No such file or directory". I had an idea to reinstall Biostrings using force = TRUE, but it didn't help. -- Dario Strbenac University of Sydney Camperdown NS

[Bioc-devel] RELEASE_3_13 is now available for bioconductor_docker

2021-05-24 Thread Nitesh Turaga
Hello Developers, The Bioconductor docker images have been updated to reflect the latest release. For more details on how to use the docker image, http://bioconductor.org/help/docker/ . - 'bioconductor/bioconductor_docker:RELEASE_3_13' is the new image (Bioc 3.13 and R version 4.1.0). - 'bioc

[Bioc-devel] Nominations for Bioconductor 2021 Awards

2021-05-24 Thread Kern, Lori
The deadline for nominations for the Bioconductor 2021 Annual Awards is a week away: May 31, 2021. We are excited to recognize those making significant outstanding contributions to the Bioconductor community. Up to four awardees will be selected, each having contributed to the project in an out

[Bioc-devel] C++ parallel computing

2021-05-24 Thread Oleksii Nikolaienko
Dear Bioc team, I'd like to ask for your advice on the parallelization within a Bioc package. Please point me to a better place if this mailing list is not appropriate. After a bit of thinking I decided that I'd like to parallelize processing at the level of C++ code. Would you strongly recommend n

Re: [Bioc-devel] VariantAnnotation Installation Compile Error

2021-05-24 Thread Vincent Carey
Thanks for the report. I just installed from source successfully with > sessionInfo() R version 4.1.0 Patched (2021-05-23 r80366) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS (fossa-melisa X20) Matrix products: default BLAS: /home/stvjc/R-4-1-dist/lib/R/lib/libRblas.s