I think one of the major changes recently is setting stringsAsFactors option to FALSE by default.
Best, Alexey On Fri, Mar 20, 2020 at 12:48 AM Charles Warden <cwar...@coh.org> wrote: > Hi Lori, > > Thank you very much. > > If I use R-4.0 (instead of R-3.6), then I can reproduce the error message. > > I will work in figuring out why the code works with R-3.6 but not R-4.0, > but it seems like this might affect other packages as well (since I > received error messages for 2 out of 2 of the Bioconductor packages that I > contributed to). > > Do you have any general suggestions of what types of new errors might be > encountered from using R-4.0? > > Thanks Again, > Charles > > From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org] > Sent: Thursday, March 19, 2020 1:41 PM > To: bioc-devel@r-project.org; Charles Warden <cwar...@coh.org> > Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message > > Yes that is the correct version of R to use. Thank you for taking the time > to make sure everything is correct to debug. We appreciate your effort and > contributors to bioconductor. > Get Outlook for Android< > https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$ > > > > ________________________________ > From: Charles Warden <cwar...@coh.org<mailto:cwar...@coh.org>> > Sent: Thursday, March 19, 2020 4:37:52 PM > To: Shepherd, Lori <lori.sheph...@roswellpark.org<mailto: > lori.sheph...@roswellpark.org>>; bioc-devel@r-project.org<mailto: > bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto: > bioc-devel@r-project.org>> > Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message > > > Hi Lori, > > > > Thank you very much for your response. > > > > I was testing building the Bioconductor development branch, but I was > using R-3.6. > > > > On the Ubuntu server where I have all the necessary dependencies > configured, I tested compiling R-devel but it didn't exactly say R-4.0. > > > > So, in order to see if I can reproduce the error, I want to make sure I am > using the same version of R: > > > > On the R website, it says "R version 4.0.0 (Arbor Day) prerelease versions< > https://urldefense.com/v3/__http:/cran.r-project.org/src/base-prerelease__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVnoU6OsCs$> > will appear starting Tuesday 2020-03-24. Final release is scheduled for > Friday 2020-04-24.", but I can download prerelease files from the following > page: > > > > https://cran.r-project.org/src/base-prerelease/< > https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$ > > > > > > I tested compiling the R-devel.tar.gz file. I think that completed > without errors, but the version of R is reported as "R Under development > (unstable) (2020-03-18 r78002)". So, I am not sure if this is correct. > > > > Is this the correct version of R to try and reproduce the error on my own > computer? If not, can you please describe which file I should be using? I > would like to install this separately from R 3.6 (in case the version of R > affects other packages as well). > > > > Thank You, > > Charles > > > > From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org] > Sent: Thursday, March 19, 2020 10:48 AM > To: Charles Warden <cwar...@coh.org<mailto:cwar...@coh.org>>; > bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> > Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message > > > > It is not okay to ignore the emails you are getting. You need to > investigate to find out if the ERROR is from your package or a package you > depend on. While you have not made changes to the package, R has made a > lot of changes to its base code that have broken a lot of packages. Most > of the changes are being documented here > > > > http://bioconductor.org/developers/how-to/troubleshoot-build-report/< > https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALMS8EdUs$ > > > > > > > > Please remember that your github version of the repo is different than our > bioconductor git.bioconductor.org server. > > http://bioconductor.org/developers/how-to/git/< > https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALKJUJjjp$ > > > > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/< > https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALF7NFkcT$ > > > > > > I can reproduce this locally on my computer. You will need to be using R > 4.0 and Bioc 3.11 version of packages. > > > > I ran R CMD Sweave COHCAP.Rnw to produce the R code in COHCAP.R > > > > > > > library(COHCAP) > > Loading required package: WriteXLS > > Loading required package: COHCAPanno > > Loading required package: RColorBrewer > > Loading required package: gplots > > > > Attaching package: 'gplots' > > > > The following object is masked from 'package:stats': > > > > lowess > > > > > source("COHCAP.R", echo=TRUE) > > > > > ### R code from vignette source > '/home/lori/b/Rpacks/COHCAP/vignettes/COHCAP.Rnw' > > > > > > ################################################### > > > ### cod .... [TRUNCATED] > > > > > dir = system.file("extdata", package="COHCAP") > > > > > beta.file = file.path(dir,"GSE42308_truncated.txt") > > > > > sample.file = file.path(dir,"sample_GSE42308.txt") > > > > > expression.file = > file.path(dir,"expression-Average_by_Island_truncated.txt") > > > > > project.folder = getwd() > > > > > project.name = "450k_avg_by_island_test" > > > > > ################################################### > > > ### code chunk number 2: annotation > > > ################################################### > > > be .... [TRUNCATED] > > [1] 173 7 > > [1] 172 5 > > [1] 172 11 > > > > > ################################################### > > > ### code chunk number 3: site > > > ################################################### > > > filtered .... [TRUNCATED] > > [1] "Reading Sample Description File...." > > [1] 172 6 > > [1] 172 6 > > [1] "Differential Methylation Stats for 2 Groups with Reference" > > [1] 172 5 > > [1] 172 10 > > > > [1] 172 10 > > [1] 34 10 > > [1] 34 10 > > > > > ################################################### > > > ### code chunk number 4: island > > > ################################################### > > > island .... [TRUNCATED] > > [1] "Reading Sample Description File...." > > [1] 172 6 > > [1] 172 6 > > [1] "Group: mutant" "Group: parental" > > [1] "Checking CpG Site Stats Table" > > [1] 34 10 > > [1] 29 10 > > [1] 5 > > [1] "Average CpG Sites per CpG Island" > > [1] "Differential Methylation Stats for 2 Groups with Reference" > > [1] 4 8 > > [1] 4 8 > > [1] "There are 4 differentially methylated islands" > > [1] 4 8 > > [1] 4 8 > > [1] "Plotting Significant Islands Box-Plots.." > > > > > ################################################### > > > ### code chunk number 5: integrate > > > ################################################### > > > COH .... [TRUNCATED] > > [1] 4 8 > > [1] 4 8 > > > > [1] 4 > > [1] 1.777472e-06 1.706586e-06 2.418011e-06 2.014309e-07 > > [1] 4 > > [1] 4 > > [1] "4 significant correlations" > > [1] "Plotting Correlated Genes...." > > [1] 4 14 > > Error in plot.xy(xy, type, ...) : invalid color name 'parental' > > > > > > > traceback() > > 8: plot.xy(xy, type, ...) > > 7: plot.default(expr, methyl, pch = 20, col = labelColors, main = > paste(gene, > > " (p=", round(cor.test(expr, methyl, na.action = na.rm)$p.value, > > digits = 2), " ,r=", round(cor.test(expr, methyl, na.action = > na.rm)$estimate, > > digits = 2), ")", sep = "")) > > 6: plot(expr, methyl, pch = 20, col = labelColors, main = paste(gene, > > " (p=", round(cor.test(expr, methyl, na.action = na.rm)$p.value, > > digits = 2), " ,r=", round(cor.test(expr, methyl, na.action = > na.rm)$estimate, > > digits = 2), ")", sep = "")) > > 5: COHCAP.integrate.avg.by.island(island.list, project.name, > project.folder, > > expression.file, sample.file) at COHCAP.R#40 > > 4: eval(ei, envir) > > 3: eval(ei, envir) > > 2: withVisible(eval(ei, envir)) > > 1: source("COHCAP.R", echo = TRUE) > > > > > > It is your job as a maintainer to try and reproduce and fix this ERROR. > > If you continue having trouble or feel like the package is failing because > of one of your dependencies please respond back here for follow up > discussion or comments. Please do not assume it comes from a dependency > without investigating. > > > > Hope this helps get you started. > > > > Cheers, > > > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > 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 Charles Warden < > cwar...@coh.org<mailto:cwar...@coh.org>> > Sent: Tuesday, March 17, 2020 1:36 PM > To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> < > bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> > Subject: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message > > > > Hi, > > I recently received error messages for 2 packages. As a > worst-case-scenario, it is acceptable if the sRAP package had to be > removed. However, I need to resolve the issue for the COHCAP package. > > This is odd because I don't think I have updated either package in the > last year or so. In fact, if I check the CHANGES file in the COHCAP > package, the last change I manually noted was v1.29.3, which I can see was > added to the GitHub version of the code on 3/2/2019: > > https://github.com/cwarden45/COHCAP/commits/master/CHANGES< > https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALNsjGd0E$ > > > > I can successfully install the package, with either the GitHub or > Bioconductor instructions. However, I want to correct the error because I > don't want the Bioconductor package to be removed. > > I had some dependency issues on some systems related to the PDF generation > (which I would usually ignore). However, if I run "R CMD build" on an > Ubuntu system where I have all dependencies installed, I don't get any > error message: > > $ R CMD build COHCAP > * checking for file 'COHCAP/DESCRIPTION' ... OK > * preparing 'COHCAP': > * checking DESCRIPTION meta-information ... OK > * cleaning src > * installing the package to build vignettes > * creating vignettes ... OK > Warning: 'inst/doc' files > 'COHCAP.Rnw', 'COHCAP.pdf', 'COHCAP.R' > ignored as vignettes have been rebuilt. > Run R CMD build with --no-build-vignettes to prevent rebuilding. > * cleaning src > * checking for LF line-endings in source and make files and shell scripts > * checking for empty or unneeded directories > * building 'COHCAP_1.33.0.tar.gz' > > I am using the development version, which I thought should match what was > being tested for the BioC 3.11 error message. > > Can you please either tell me what I need to do to reproduce (and then > correct) this error, or confirm that it is OK to ignore the e-mails that I > have received recently? > > Thank You, > Charles > > Charles Warden, Bioinformatics Specialist > Integrative Genomics Core > City of Hope National Medical Center > Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016) > Room 1086 > Internal Ext: 80375 | Direct: 626-218-0375 > Work-From-Home Cell: 404-316-0012 > > ---------------------------------------------------------------------- > ------------------------------------------------------------ > -SECURITY/CONFIDENTIALITY WARNING- > > This message and any attachments are intended solely for the individual or > entity to which they are addressed. This communication may contain > information that is privileged, confidential, or exempt from disclosure > under applicable law (e.g., personal health information, research data, > financial information). Because this e-mail has been sent without > encryption, individuals other than the intended recipient may be able to > view the information, forward it to others or tamper with the information > without the knowledge or consent of the sender. If you are not the intended > recipient, or the employee or person responsible for delivering the message > to the intended recipient, any dissemination, distribution or copying of > the communication is strictly prohibited. If you received the communication > in error, please notify the sender immediately by replying to this message > and deleting the message and any accompanying files from your system. If, > due to the security risks, you do not wish to rec > eive further communications via e-mail, please reply to this message and > inform the sender that you do not wish to receive further e-mail from the > sender. (LCP301) > ------------------------------------------------------------ > > [[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< > https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/bioc-devel__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALLPn4Ueu$ > > > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
