[Bioc-devel] SSL error on Ubuntu 20.04
Dear BioC community, We were recently informed that a multilayered bug due to an increased security level in Ubuntu 20.04, configuration issues on server side and a bug in OpenSSL 1.1.1 caused our packages to fail on Ubuntu 20.04 with the following error: error:14094410:SSL routines:ssl3_read_bytes:sslv3 alert handshake failure This affects the two packages I maintain, rfaRm and ncRNAtools. As a temporary fix, we were suggested to use HTTP instead of HTTPS. However, some of the web resources accessed with our packages do not seem to be accessible via HTTP. This is reflected in the latest build for rfaRm for example (http://bioconductor.org/checkResults/devel/bioc-LATEST/rfaRm/) , which fails as a consequence of all the URLs being changed to the “http” version instead of “https”. The problem seems to have been discussed here https://github.com/Ensembl/ensembl-rest/issues/427 , with a temporary fix suggested here https://askubuntu.com/questions/1233186/ubuntu-20-04-how-to-set-lower-ssl-security-level . However, this seems to involve changing some openssl options through the openssl config file. We are unsure on whether this temporary fix could be implemented from within our package. We would greatly appreciate any guidance on how to implement it, or on any other alternative temporary workarounds. Thanks a lot in advance! Best wishes, Lara [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Package failing specifically on OS X - Java version? How to debug?
Hello BioC community, Our package build fails specifically on merida, the OS X machine. I suspect the issue is due to Java version incompatibility for that machine (based on the nature of the error message and ongoing Java-related issues). https://bioconductor.org/checkResults/3.12/bioc-LATEST/netDx/merida1-buildsrc.html Running the build locally on my OS X 10.13.6 with R4.0 and Java 1.8 works successfully (build and check both pass). I even set up the .Renviron.bioc file for reproducibility, and everything runs through without errors. To debug this, I enabled verbose messaging when committing on the 28th, but don't see the printouts in the subsequent build results from last night. I just further increased verbose messages - how can I get to the bottom of the error? Also, what is the Java version used on merida? I believe the issue has been fixed for Java 11 and 14, unless something else changed re: Java setup on this machine. Thanks,Shraddha [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Git pack file greater than 5MB
Hi all, We have a package that is ready for submission, but when running BiocCheck a warning is generated noting that "The following files are over 5MB in size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and run git gc which reduced the file size from 5.2 to 5.1MB, but I have been unable to reduce it further. I'm reaching out to determine if this is an issue, and if so to ask for recommendations for solving it. Currently, the only solution I've come up with is to rewrite the repository's history using a tool like "git-filter-repo", but this is a more drastic action than I would prefer to take. I would greatly appreciate any advice on the matter. Thank you, Max McGrath [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
