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

Thu Mar 19 23:03:02 CET 2020

Hi Alexey,

Thank you very much – I will look into that.  It does look like at least 1 demo dataset is being read incorrectly.

Sincerely,
Charles

From: Alexey Sergushichev [mailto:alsergbox using gmail.com]
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden <cwarden using coh.org>
Cc: Shepherd, Lori <Lori.Shepherd using roswellpark.org>; bioc-devel using 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 using coh.org<mailto: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<mailto:Lori.Shepherd using RoswellPark.org>]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>; Charles Warden <cwarden using coh.org<mailto: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><mailto: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<mailto:Lori.Shepherd using RoswellPark.org>>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org><mailto: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><mailto: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!-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 using RoswellPark.org<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><mailto:cwarden using coh.org<mailto:cwarden using coh.org>>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org><mailto: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!-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.

http://bioconductor.org/developers/how-to/git/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSWmrZ5ZV$><https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALKJUJjjp$>

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!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSfOmQzUp$><https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALF7NFkcT$>

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<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 using r-project.org<mailto:bioc-devel-bounces using r-project.org><mailto: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><mailto: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><mailto: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><mailto: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!-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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