[R-pkg-devel] dependency on a bioconductor package

(don't forget to 'reply all', so that others may benefit / contribute to 
the conversation).

You or one of the packages your package depends on must Depend: or 
Import: BiocInstaller. If it is your package, then you should no longer 
do so. If it is one of the packages your package depends on, then the 
responsible thing to do is to contact the author of that package and 
indicate that they should update their package to no longer depend on 
BiocInstaller.

I do not know how the CRAN team will view this warning; I would guess 
that, if it is not directly under your control, then they will not be 
overly concerned about it.

Martin

On 10/5/18 1:35 PM, maialba at alumni.uv.es wrote:

Hello Morgan,

thank you for the replay but, how should I solve the problem in my package? I did install CAMERA using BiocManager in my computer and my package works fine. I do not get any warnings when I run R CDM check but the problem appears when I try to submit it to CRAN.

Maribel

BiocInstaller has been replaced by the CRAN package BiocManager; the
appropriate way to install Bioconductor packages is
BiocManager::install(). See the vignette at

https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManagerhtml

Martin


On 10/5/18 5:36 AM, maialba at alumni.uv.es wrote:

I do not know how to solve this warning. I guess it comes from the package dependency on CAMERA (bioconductor) but I can?t solve it.

https://win-builder.r-project.org/incoming_pretest/LipidMS_1.0.0_20181005_103151/Windows/00check.log>

requiredByCAMERA <- tools::package_dependencies("CAMERA",

directlyRequired <- tools::package_dependencies(requiredByCAMERA)
names(directlyRequired)[ vapply(directlyRequired,

directlyRequired$affy

getOption("repos")

(don't forget to 'reply all', so that others may benefit / contribute to
the conversation).

You or one of the packages your package depends on must Depend: or Import:
BiocInstaller. If it is your package, then you should no longer do so. If
it is one of the packages your package depends on, then the responsible
thing to do is to contact the author of that package and indicate that they
should update their package to no longer depend on BiocInstaller.

I do not know how the CRAN team will view this warning; I would guess
that, if it is not directly under your control, then they will not be
overly concerned about it.

Martin

On 10/5/18 1:35 PM, maialba at alumni.uv.es wrote:

Hello Morgan,

thank you for the replay but, how should I solve the problem in my
package? I did install CAMERA using BiocManager in my computer and my
package works fine. I do not get any warnings when I run R CDM check but
the problem appears when I try to submit it to CRAN.

Maribel


BiocInstaller has been replaced by the CRAN package BiocManager; the

appropriate way to install Bioconductor packages is
BiocManager::install(). See the vignette at

https://cran.r-project.org/web/packages/BiocManager/vignette
s/BiocManagerhtml

Martin


On 10/5/18 5:36 AM, maialba at alumni.uv.es wrote:

I do not know how to solve this warning. I guess it comes from the
package dependency on CAMERA (bioconductor) but I can?t solve it.

https://win-builder.r-project.org/incoming_pretest/LipidMS_1
.0.0_20181005_103151/Windows/00check.log>

It looks like affy is the culprit.

 > requiredByCAMERA <- tools::package_dependencies("CAMERA", 

recursive=TRUE)$CAMERA

 > directlyRequired <- tools::package_dependencies(requiredByCAMERA)
 > names(directlyRequired)[ vapply(directlyRequired, 

function(x)"BiocInstaller"%in%x, FUN.VALUE=NA) ]
[1] "affy"

 > directlyRequired$affy

 ?[1] "BiocGenerics"? ?"Biobase"? ? ? ? "affyio"        
 ?"BiocInstaller"? "graphics"? ? ? ?"grDevices"
 ?[7] "methods"? ? ? ? "preprocessCore" "stats"? ? ? ? ? "utils"        
 ? "zlibbioc"

 > getOption("repos")

 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? CRAN                  
 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?BioCsoft
 ? ? ? ? ? ? ? ? ? ? ? ? ?"https://cloud.r-project.org"    
"http://www.bioconductor.org/packages/release/bioc"
 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?BioCann                  
 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? BioCexp
"http://bioconductor.org/packages/3.5/data/annotation" 
"http://bioconductor.org/packages/3.5/data/experiment"


Bill Dunlap
TIBCO Software
wdunlap tibco.com <http://tibco.com>

On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin <mtmorgan.bioc at gmail.com 
<mailto:mtmorgan.bioc at gmail.com>> wrote:

    (don't forget to 'reply all', so that others may benefit /
    contribute to the conversation).

    You or one of the packages your package depends on must Depend: or
    Import: BiocInstaller. If it is your package, then you should no
    longer do so. If it is one of the packages your package depends on,
    then the responsible thing to do is to contact the author of that
    package and indicate that they should update their package to no
    longer depend on BiocInstaller.

    I do not know how the CRAN team will view this warning; I would
    guess that, if it is not directly under your control, then they will
    not be overly concerned about it.

    Martin

    On 10/5/18 1:35 PM, maialba at alumni.uv.es
    <mailto:maialba at alumni.uv.es> wrote:

        Hello Morgan,

        thank you for the replay but, how should I solve the problem in
        my package? I did install CAMERA using BiocManager in my
        computer and my package works fine. I do not get any warnings
        when I run R CDM check but the problem appears when I try to
        submit it to CRAN.

        Maribel


            BiocInstaller has been replaced by the CRAN package
            BiocManager; the
            appropriate way to install Bioconductor packages is
            BiocManager::install(). See the vignette at

            https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManagerhtml
            <https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManagerhtml>

            Martin


            On 10/5/18 5:36 AM, maialba at alumni.uv.es
            <mailto:maialba at alumni.uv.es> wrote:

                I do not know how to solve this warning. I guess it
                comes from the package dependency on CAMERA
                (bioconductor) but I can?t solve it.

                https://win-builder.r-project.org/incoming_pretest/LipidMS_1.0.0_20181005_103151/Windows/00check.log
                <https://win-builder.r-project.org/incoming_pretest/LipidMS_1.0.0_20181005_103151/Windows/00check.log>>