You could always reach out to the maintainer to try and get them interested again.
Or reach out on the mailing list or support site to see if anyone else is interested in taking over maintaining the package. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Nicolas Descostes <nicolas.descos...@gmail.com> Sent: Tuesday, May 15, 2018 8:20:47 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] htSeqTools and giniCoverage error I guess I should make my package independent of it then, but that's going to ask some work. That's very unfortunate... 2018-05-15 7:24 GMT-04:00 Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>: What is your sessionInfo()? This was corrected in version 1.27.1 of the package so you could try updating to that version. However, htSeqTools is currently deprecated in Release Bioc 3.7 and currently scheduled to be removed in Bioc 3.8 as the maintainer has be inactive in maintaining the package and unresponsive to our requests to fix their package. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Nicolas Descostes <nicolas.descos...@gmail.com<mailto:nicolas.descos...@gmail.com>> Sent: Sunday, May 13, 2018 1:35:05 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Cc: oscar.re...@irbbarcelona.org<mailto:oscar.re...@irbbarcelona.org> Subject: [Bioc-devel] htSeqTools and giniCoverage error Dear all, I am using htseqtools on the devel version and I get the following error when using giniCoverage: test <- lapply(endoExoBamlist, function(bam_files){ return(lapply(bam_files, function(bamfile){ ga <- if(paired) granges(readGAligmentPairs(bamfile)) else granges(readGAlignments(bamfile)) })) }) test2 <- lapply(test, GRangesList) giniCoverage(sample=test2[[1]]) Simulating uniformily distributed data Error: The RangesList() constructor is defunct. Please coerce to IRangesList instead e.g. do 'as(list(x1, x2), "IRangesList")' instead of 'RangesList(x1, x2)'. Alternatively, you can use the IRangesList() constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See '?IRangesList' for more information. In addition: Warning messages: 1: The "lapply" method for RangedData objects is deprecated and won't be replaced. Please migrate your code to use GRanges or GRangesList objects instead. RangedData objects will be deprecated soon (their use has been discouraged since BioC 2.12, that is, since 2014). See IMPORTANT NOTE in ?RangedData 2: The "lapply" method for RangedData objects is deprecated and won't be replaced. Please migrate your code to use GRanges or GRangesList objects instead. RangedData objects will be deprecated soon (their use has been discouraged since BioC 2.12, that is, since 2014). See IMPORTANT NOTE in ?RangedData Looking at the code it seems that the problem is coming from the line 212 of giniCoverage.R: RD<-RangedData(RangesList(rangesl)) Would it be possible to correct this? I am using version 1.27.0 Thanks a lot, Nicolas [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
