[Bioc-devel] BioC packages NuPoP and nuCpos

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri May 24 15:02:30 CEST 2019

We do not manually replace Bioconductor packages for maintainers.  Bioconductor packages are maintained in git and you will have to push up the changes.

Please see the following documentation:


Feel free to comment back here with any further questions or if you have trouble connecting the the bioconductor git repository of your packages.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jiping Wang <jzwang using northwestern.edu>
Sent: Friday, May 24, 2019 8:51:22 AM
To: bioc-devel using r-project.org
Cc: Prof Brian Ripley; Liqun Xi
Subject: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Bioc-devel] BioC packages NuPoP and nuCpos


   We have made minor revision of the NuPoP package such that the revised version does not pass character strings from R to Fortran. This revised package has been tested working properly. We would like to replace the NuPoP package at Bioconductor.org by the attached one.  Please advise if anything else we should do or correct. Thanks for help.

Ji-Ping Wang, Ph.D.
Department of Statistics and Molecular BioSciences
Northwestern University

On 5/22/19, 1:10 AM, "Prof Brian Ripley" <ripley using stats.ox.ac.uk> wrote:

    These now give in R-patched and R-devel (and BioC 3.9 and 3.10)

    NuPoP.Rcheck/NuPoP-Ex.Rout:  passing a char vector to .Fortran is not
    nuCpos.Rcheck/nuCpos-Ex.Rout:  passing a char vector to .Fortran is not

    This come from the NEWS item

         • The use of a character vector with .Fortran() is formally
           deprecated and gives a non-portability warning.  (It has long
           been strongly discouraged in ‘Writing R Extensions’.)

    (It is even less portable than we had previously thought.)  Please avoid
    it (and it is liable to be removed before too long): the preferred way
    to do that is to use .Call with a C wrapper calling the Fortran code.

    Brian D. Ripley,                  ripley using stats.ox.ac.uk
    Emeritus Professor of Applied Statistics, University of Oxford

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