[R-pkg-devel] dependency on a bioconductor package
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> __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] dependency on a bioconductor package
BiocInstaller has been replaced by the CRAN package BiocManager; the appropriate way to install Bioconductor packages is BiocManager::install().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/BiocManager.html Martin On 10/5/18 5:36 AM, maia...@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> __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [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, maia...@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 Maribel BiocInstaller has been replaced by the CRAN package BiocManager; the appropriate way to install Bioconductor packages is BiocManager::install().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, maia...@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> __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] dependency on a bioconductor package
(sorry about the replay, my mistake) ok, then I guess that is the problem...I do not depend on BiocInstaller so it must be one of my dependencies. Thank you very much! Maribel > (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, maia...@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, maia...@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> > >>> > >>> __ > >>> R-package-devel@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > >> __ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > > > > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] dependency on a bioconductor package
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
On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin
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, maia...@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, maia...@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>
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>>
>>
>>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] dependency on a bioconductor package
Bioconductor has a release and a devel branch, with the idea that new
features are introduced into 'devel'. The transition to use BiocManager
is a new feature introduced into devel, and BiocInstaller has a
deprecation message added in devel only. It follows that win-builder is
using bioc-devel (this is reasonable; our next release is at the end of
this month), and that we'd look for use of BiocInstaller in devel
packages. affy is itself a 'core team' package, and we have removed use
of BiocInstaller from that.
But let's see... the 'release' branch has
> dput(repos)
c(BioCsoft = "https://bioconductor.org/packages/3.7/bioc";, BioCann =
"https://bioconductor.org/packages/3.7/data/annotation";,
BioCexp = "https://bioconductor.org/packages/3.7/data/experiment";,
BioCworkflows = "https://bioconductor.org/packages/3.7/workflows";,
CRAN = "https://cran.rstudio.com";)
> db = available.packages(repos=repos)
> revdeps = tools::package_dependencies("LipidMS", db, recursive=TRUE)
> "BiocInstaller" %in% unlist(revdeps)
[1] TRUE
and indeed BiocInstaller is problematic (but BiocInstaller in the
release branch doesn't generate the warning...) (also, I'm not sure
about the '3.5' components of your annotation / experiment repos, these
should be the same as the main repository).
On the other hand in our devel branch
> repos = sub("3.7", "3.8", repos)
> db = available.packages(repos=repos)
> revdeps = tools::package_dependencies("LipidMS", db, recursive=TRUE)
> "BiocInstaller" %in% unlist(revdeps)
[1] FALSE
So at least for packages that are current in CRAN and in the devel
branch of Bioconductor there is no use of BiocInstaller.
I'm not exactly sure where this leaves us...
Martin
On 10/5/18 2:26 PM, William Dunlap wrote:
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
On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin > 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, maia...@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, maia...@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
>
___
