[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Martin, I am currently having difficulty reproducing my earlier error (which I think didn?t even get to the step of testing the demo code). So, I think the short answer is that I should just use version 1.33.1. In my search history, I can tell that I Googled "R Malformed package version," so I think that was part of the earlier message that I got. For what is worth, I think this is what gave me the idea to change the version numbering system: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file However, if I am not currently getting an error message, then I won't worry about it. Thank you very much for your help! Sincerely, Charles -----Original Message----- From: Martin Morgan <mtmorgan.bioc at gmail.com> Sent: Friday, March 20, 2020 1:09 PM To: Charles Warden <cwarden at coh.org>; Alexey Sergushichev <alsergbox at gmail.com> Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message Can you be precise about the concern about 1.33.1 as a version number (what precise note / error / warning you received)? This scheme is very standard for package versions, and as you see enforced (for many years!) by Bioconductor. Martin ?On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" <bioc-devel-bounces at r-project.org on behalf of cwarden at coh.org> wrote: Hi Everybody, I think changing that read.table() parameter fixed the main issue. However, when I tested my code, R used a different way to note versions in R-v.4.0.0. For example, in order to clear a message from ?R CMD check? or ?R CMD build?, I had to say the version was 1.33-1 (instead of 1.33.1). I uploaded those changes to GitHub and tested an R-3.6 installation, and that was OK. However, when I am working on merging the GitHub and Bioconductor branches, I get the following error message: ?Remote: Error: Illegal version bump from ?1.33.0? to ?1.33-1?? Is this going to be changed in Bioconductor, or should I see if this is only a NOTE or WARNING (and submit the package as version 1.33.1)? Thank You, Charles From: Alexey Sergushichev <alsergbox at gmail.com> Sent: Thursday, March 19, 2020 3:00 PM To: Charles Warden <cwarden at coh.org> Cc: Shepherd, Lori <Lori.Shepherd at roswellpark.org>; bioc-devel at r-project.org Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message 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 at coh.org<mailto:cwarden at 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 at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>; Charles Warden <cwarden at coh.org<mailto:cwarden at 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$>
From: Charles Warden <cwarden at coh.org<mailto:cwarden at coh.org><mailto:cwarden at coh.org<mailto:cwarden at coh.org>>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>>>; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>>>; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Lori,
Thank you very much for your response.
I was testing building the Bioconductor development branch, but I was using R-3.6.
On the Ubuntu server where I have all the necessary dependencies configured, I tested compiling R-devel but it didn't exactly say R-4.0.
So, in order to see if I can reproduce the error, I want to make sure I am using the same version of R:
On the R website, it says "R version 4.0.0 (Arbor Day) prerelease versions<https://urldefense.com/v3/__http:/cran.r-project.org/src/base-prerelease__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVnoU6OsCs$> 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://urldefense.com/v3/__https://cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5ckE5viQC$ <https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSaed1B9J$><https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$>
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 at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>]
Sent: Thursday, March 19, 2020 10:48 AM
To: Charles Warden <cwarden at coh.org<mailto:cwarden at coh.org><mailto:cwarden at coh.org<mailto:cwarden at coh.org>>>; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at 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
https://urldefense.com/v3/__http://bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5ckm9ArKf$ <https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSapsB6_9$><https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALMS8EdUs$>
Please remember that your github version of the repo is different than our bioconductor git.bioconductor.org<https://urldefense.com/v3/__http:/git.bioconductor.org__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSckTNGQt$> server.
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I can reproduce this locally on my computer. You will need to be using R 4.0 and Bioc 3.11 version of packages.
I ran R CMD Sweave COHCAP.Rnw to produce the R code in COHCAP.R
> library(COHCAP)
Loading required package: WriteXLS
Loading required package: COHCAPanno
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
> source("COHCAP.R", echo=TRUE)
> ### R code from vignette source '/home/lori/b/Rpacks/COHCAP/vignettes/COHCAP.Rnw'
>
> ###################################################
> ### cod .... [TRUNCATED]
> dir = system.file("extdata", package="COHCAP")
> beta.file = file.path(dir,"GSE42308_truncated.txt")
> sample.file = file.path(dir,"sample_GSE42308.txt")
> expression.file = file.path(dir,"expression-Average_by_Island_truncated.txt")
> project.folder = getwd()
> project.name<https://urldefense.com/v3/__http:/project.name__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSRpln5M0$> = "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<https://urldefense.com/v3/__http:/COHCAP.integrate.avg.by__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSYVza8qp$>.island(island.list, project.name<https://urldefense.com/v3/__http:/project.name__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSRpln5M0$>, 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 at r-project.org<mailto:bioc-devel-bounces at r-project.org><mailto:bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>>> on behalf of Charles Warden <cwarden at coh.org<mailto:cwarden at coh.org><mailto:cwarden at coh.org<mailto:cwarden at coh.org>>>
Sent: Tuesday, March 17, 2020 1:36 PM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto:bioc-devel at 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://urldefense.com/v3/__https://github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cn-PlqxU$ <https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSURsP8QF$><https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALNsjGd0E$>
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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