[Bioc-devel] [External] Re: updating package on the development version

Dwivedi, Bhakti bh@kt|@dw|ved| @end|ng |rom emory@edu
Sat Jun 20 22:38:22 CEST 2020

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.


On 6/20/20, 9:29 AM, "Martin Morgan" <mtmorgan.bioc using 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)


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


        From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
        Sent: Friday, June 19, 2020 7:00 AM
        To: Dwivedi, Bhakti <bhakti.dwivedi using emory.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
        Subject: [External] Re: updating package on the development version

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        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.


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


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        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> on behalf of Dwivedi, Bhakti <bhakti.dwivedi using emory.edu>
        Sent: Thursday, June 18, 2020 4:24 PM
        To: bioc-devel using r-project.org <bioc-devel using r-project.org>
        Subject: [Bioc-devel] updating package on the development version


        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://secure-web.cisco.com/16G6QGHF8mpcsjsZBAAOMWj_a4_z0hmCZlj_TnB4TkGbw3lcmQkHHEjOqoyzLjoOMRn1aXjkTjb5avdzEYK8TvzOinzWcd9qWMiZtKViQYb59qlnna0b2zm1kpo9g5N-CAfehjdWj1aJjXXzU0Hr8DFvi9egMpJ8mJfKVtjZIxiNHpmVpAVpylYQTaAhqJ00j8m4g_-g32S9NI3JBhD0t4AqG-FOe6_XBx_MtqxawqmeCbMmzb7ACMy2fDyMtMWJN_8CFfp0MxJHYuURFn_zJFFrA_8OC5MS263jFlJ4tkGIjjP4i3l23Pk98aN0pleohwwTq6H5r4yXwIUIJZ1UtYixHkMKeMzfgh7Mx2jvPXCs/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F

        But, I do not see the change on the bioconductor development version http://secure-web.cisco.com/1BfCJ7lm3FxR9215Gg0wJ4F_f-OUbGZlfSX7Ht1DBVyLt-CZZV-KC00A6xzrjCgeuhtuBWXSLpVmnjtVS2OXstGp5uPIT9ZrzhInLClCHaban0Vu4Cgjcat6pKhyv0_mkXT3BDemwUsYEc-n5Ci7Hg5ZyWVJNiFi8RXqmJZ7jivCEJbsbmPLkns3Aqlvm7sIpUsbyrHU_3sZB9ThrXyRAg1i6MYujiums1jeOJyKkH8xJ8rzlg4SZosumRATLEpNxRcqx0vJYGendXkAFaOLdducAMIKK1cFguQP3GuBIZGWXXTBajVSvf3AtXUEkgCGHMX_okMSo4UDIdulKBzh1bxvq1SjHw4IhYlMYjTUg9KI/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FGISPA.html. Where can I view the changes and make sure it passed all the checks?



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