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 <http://tibco.com>
On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin <mtmorgan.b...@gmail.com
<mailto:mtmorgan.b...@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, maia...@alumni.uv.es
<mailto: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
<https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManagerhtml>
Martin
On 10/5/18 5:36 AM, maia...@alumni.uv.es
<mailto: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
<https://win-builder.r-project.org/incoming_pretest/LipidMS_1.0.0_20181005_103151/Windows/00check.log>>
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