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[Bioc-devel] updating package on the development version

5 messages · Shepherd, Lori, Martin Morgan, Dwivedi, Bhakti

Original
Dwivedi, Bhakti
# 
Hi,

I am trying to update previous release of my package (GISPA) on the development version.

I pushed the changes and new release GISPA 1.13.1 following https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

But, I do not see the change on the bioconductor development version http://bioconductor.org/packages/devel/bioc/html/GISPA.html. Where can I view the changes and make sure it passed all the checks?

Regards,
Bhakti



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Shepherd, Lori
# 
Please see this post indicating that we are having trouble with our website and are in process of fixing it.  We have located the issue and pushed a fix and once applied the landing pages should generate properly.

https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html


Please check the build reports for the version numbers that are being used to build the package.

http://bioconductor.org/checkResults/

Keeping in mind there can be up to a 48 hour delay to see the results as described here:

http://bioconductor.org/developers/how-to/troubleshoot-build-report/

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Dwivedi, Bhakti
# 
Thank you for your response.

Quick question, I am getting the warning and below error message. any suggestions or is there a link that I can follow to get help and fix it?

** installing vignettes
Warning in file(con, "w") :
  cannot open file '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GISPA/00new/GISPA/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection


Regards,
Bhakti
Martin Morgan
# 
Does your vignette try to install a package? It should not.

You can delete the 'lock file with

path = "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GISPA"
unlink(path, recursive = TRUE)

Martin

?On 6/19/20, 2:53 PM, "Bioc-devel on behalf of Dwivedi, Bhakti" <bioc-devel-bounces at r-project.org on behalf of bhakti.dwivedi at emory.edu> wrote:

    Thank you for your response.

    Quick question, I am getting the warning and below error message. any suggestions or is there a link that I can follow to get help and fix it?

    ** installing vignettes
    Warning in file(con, "w") :
      cannot open file '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GISPA/00new/GISPA/doc/index.html': No such file or directory
    Error in file(con, "w") : cannot open the connection


    Regards,
    Bhakti
Dwivedi, Bhakti
# 
Hi Martin,

Thank you so much for your suggestions.

I fixed the errors as below and then ran the build/install/check commands and didn't get any error. 

Submitting the package, hoping by tomorrow everything should pass OK.

Regards,
Bhakti
?On 6/20/20, 9:29 AM, "Martin Morgan" <mtmorgan.bioc at gmail.com> wrote:
Does your vignette try to install a package? It should not.

    You can delete the 'lock file with

    path = "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GISPA"
    unlink(path, recursive = TRUE)

    Martin
On 6/19/20, 2:53 PM, "Bioc-devel on behalf of Dwivedi, Bhakti" <bioc-devel-bounces at r-project.org on behalf of bhakti.dwivedi at emory.edu> wrote:
Thank you for your response.

        Quick question, I am getting the warning and below error message. any suggestions or is there a link that I can follow to get help and fix it?

        ** installing vignettes
        Warning in file(con, "w") :
          cannot open file '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GISPA/00new/GISPA/doc/index.html': No such file or directory
        Error in file(con, "w") : cannot open the connection


        Regards,
        Bhakti