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

Tue Mar 24 16:13:46 CET 2020

Hi Lori,

Thank you very much for your help!

Sincerely,
Charles

From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Tuesday, March 24, 2020 5:39 AM
To: Charles Warden <cwarden using coh.org>; 'Martin Morgan' <mtmorgan.bioc using gmail.com>; 'Alexey Sergushichev' <alsergbox using gmail.com>
Cc: 'bioc-devel using r-project.org' <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Thank you for your contributions to Bioconductor.  We appreciate you fixing COHCAP.

I will begin the deprecation process for sRAP;  there is no further action needed.

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: Monday, March 23, 2020 3:53 PM
To: 'Martin Morgan' <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>; 'Alexey Sergushichev' <alsergbox using gmail.com<mailto:alsergbox using gmail.com>>
Cc: 'bioc-devel using r-project.org' <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Everybody,

Thank you again for your help!

I think the issue for the COHCAP devel package has now been resolved:

http://bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/<https://urldefense.com/v3/__http:/bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/__;!!Fou38LsQmgU!4pixzueuEashd7OMaAtrxWF6J7-9ZdkNh7lA1938iAeeYvzmbMVMrX-o7Sq7$>

I had somewhat similar error messages for sRAP (which is different than COHCAP), but I am OK with sRAP being removed from the next version of Bioconductor (since it is no longer being maintained).  If you can please let me know if there is a contact that I should e-mail (beyond this mailing list, or not fixing the error), then I would appreciate that.

Thanks Again,
Charles

-----Original Message-----
From: Charles Warden
Sent: Friday, March 20, 2020 1:40 PM
To: Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>; Alexey Sergushichev <alsergbox using gmail.com<mailto:alsergbox using gmail.com>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: RE: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Martin,

That is probably what happened.

Thank you again for your help!

Sincerely,
Charles

-----Original Message-----
From: Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden <cwarden using coh.org<mailto:cwarden using coh.org>>; Alexey Sergushichev <alsergbox using gmail.com<mailto:alsergbox using gmail.com>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar, '1.33. 1' ? This generates an error

** using staged installation
Error : Invalid DESCRIPTION file

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ...

Martin

On 3/20/20, 4:28 PM, "Charles Warden" <cwarden using coh.org<mailto:cwarden using coh.org>> wrote:

    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://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$<https://urldefense.com/v3/__https:/cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$>

    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 using gmail.com<mailto:mtmorgan.bioc using gmail.com>>
    Sent: Friday, March 20, 2020 1:09 PM
    To: Charles Warden <cwarden using coh.org<mailto:cwarden using coh.org>>; Alexey Sergushichev <alsergbox using gmail.com<mailto:alsergbox using gmail.com>>
    Cc: bioc-devel using r-project.org<mailto:bioc-devel using 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 using r-project.org on behalf of cwarden using coh.org<mailto:bioc-devel-bounces using r-project.org%20on%20behalf%20of%20cwarden using 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 using gmail.com<mailto:alsergbox using gmail.com>>
        Sent: Thursday, March 19, 2020 3:00 PM
        To: Charles Warden <cwarden using coh.org<mailto:cwarden using coh.org>>
        Cc: 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>
        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<mailto:cwarden using coh.org%3cmailto: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<mailto:Lori.Shepherd using RoswellPark.org%3cmailto: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<mailto:bioc-devel using r-project.org%3cmailto:bioc-devel using r-project.org>>; Charles Warden <cwarden using coh.org<mailto:cwarden using coh.org<mailto:cwarden using coh.org%3cmailto: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%3cmailto:cwarden using coh.org>><mailto:cwarden using coh.org<mailto:cwarden using coh.org<mailto:cwarden using coh.org%3cmailto: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<mailto:Lori.Shepherd using RoswellPark.org%3cmailto:Lori.Shepherd using RoswellPark.org%3cmailto: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<mailto:bioc-devel using r-project.org%3cmailto:bioc-devel using r-project.org%3e%3cmailto:bioc-devel using r-project.org%3cmailto: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%3cmailto: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%3cmailto: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://urldefense.com/v3/__https://cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5ckE5viQC$<https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5ckE5viQC$> <https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSaed1B9J$><https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$<https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSaed1B9J$%3e%3chttps:/urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$>>

        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<mailto:Lori.Shepherd using RoswellPark.org%3cmailto: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%3cmailto:cwarden using coh.org>><mailto:cwarden using coh.org<mailto:cwarden using coh.org<mailto:cwarden using coh.org%3cmailto: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<mailto:bioc-devel using r-project.org%3cmailto:bioc-devel using r-project.org%3e%3cmailto:bioc-devel using r-project.org%3cmailto: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

        https://urldefense.com/v3/__http://bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5ckm9ArKf$<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5ckm9ArKf$> <https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSapsB6_9$><https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALMS8EdUs$<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSapsB6_9$%3e%3chttps:/urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALMS8EdUs$>>

        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.

        https://urldefense.com/v3/__http://bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cuqY629o$<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cuqY629o$> <https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSWmrZ5ZV$><https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALKJUJjjp$<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSWmrZ5ZV$%3e%3chttps:/urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALKJUJjjp$>>

        https://urldefense.com/v3/__http://bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cjaOhv-r$<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cjaOhv-r$> <https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSfOmQzUp$><https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALF7NFkcT$<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSfOmQzUp$%3e%3chttps:/urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALF7NFkcT$>>

        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%3cmailto: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%3cmailto: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%3cmailto:cwarden using coh.org>><mailto:cwarden using coh.org<mailto:cwarden using coh.org<mailto:cwarden using coh.org%3cmailto: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<mailto:bioc-devel using r-project.org%3cmailto:bioc-devel using r-project.org%3e%3cmailto:bioc-devel using r-project.org%3cmailto: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%3cmailto: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%3cmailto: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://urldefense.com/v3/__https://github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cn-PlqxU$<https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!6Z-O-2_mcUZjWMQJYI_s9IC_6Lm6oz-SyHSeDdfRtx9sSaCT8By5cn-PlqxU$> <https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSURsP8QF$><https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALNsjGd0E$<https://urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSURsP8QF$%3e%3chttps:/urldefense.com/v3/__https:/github.com/cwarden45/COHCAP/commits/master/CHANGES__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALNsjGd0E$>>

        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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