[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

[Alexey Sergushichev]

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 <cwarden using 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.Shepherd using RoswellPark.org]
> Sent: Thursday, March 19, 2020 1:41 PM
> To: bioc-devel using r-project.org; Charles Warden <cwarden using 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 <cwarden using coh.org<mailto:cwarden using coh.org>>
> Sent: Thursday, March 19, 2020 4:37:52 PM
> To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:
> Lori.Shepherd using RoswellPark.org>>; bioc-devel using r-project.org<mailto:
> bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:
> bioc-devel using 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.Shepherd using RoswellPark.org]
> Sent: Thursday, March 19, 2020 10:48 AM
> To: Charles Warden <cwarden using coh.org<mailto:cwarden using coh.org>>;
> bioc-devel using r-project.org<mailto:bioc-devel using 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-bounces using r-project.org<mailto:
> bioc-devel-bounces using r-project.org>> on behalf of Charles Warden <
> cwarden using coh.org<mailto:cwarden using coh.org>>
> Sent: Tuesday, March 17, 2020 1:36 PM
> To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <
> bioc-devel using r-project.org<mailto:bioc-devel using 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
>
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