[Bioc-devel] lumi package is not available

[Kevin RUE]

Dear T.Wang.

First of all, as a general rule, please include the sessionInfo() output
and command that caused the error to facilitate useful replies. Here I will
assume that you are using the devel branch of BioC on the latest R/BioC
setup available.

As far as I know, your problem is still a consequence of the recent
release, affecting all packages dependencies which have not passed a single
R CMD check on the new devel branch (the issue has been reported on this
mailing list for a few packages already; e.g. Biobase, now resolved). the
situation should resolve after all relevant packages pass at least one
build cycle without error:

   - For the lumi package, you can see the R CMD check failing in all
   platforms build report: http://bioconductor.org/checkResults/devel/bioc-
   LATEST/lumi/
   - Note that this is also the case for the release branch
   http://bioconductor.org/checkResults/3.4/bioc-LATEST/lumi/
   - As a result, the package was not released yet on the devel branch of
   the repository, and the landing page of the lumi package is not available
   yet either (click the lumi link in the build report above, which will take
   you to http://bioconductor.org/packages/3.5/bioc/html/lumi.html).
   - Another artifact of this situation is that the landing page of the
   release branch still claims to be the devel branch
   http://bioconductor.org/packages/3.4/bioc/html/lumi.html

Solution (as far as I know):

   - Simply wait that the package (and its dependencies) passes R CMD check
   on all platforms, which will then trigger its release on the BioC
   repository.
   - In other circumstances, I would have suggested to install the lumi
   package from the release branch in the meantime, but given the build errors
   there as well, you might have to download older sources of the package, and
   install them using "install.packages(..., repos = NULL)" rather than
   "biocLite(...)"

Last but not least, I will also point out that a quick check of the
Bioconductor Git Mirror suggests that the latest BioC release where the
lumi package code was updated is release-3.1 (
https://github.com/Bioconductor-mirror/lumi/tree/release-3.1). Maybe some
code updates are overdue now for package to build succesfully.

Kind regads,
Kevin








On Fri, Oct 28, 2016 at 9:20 AM, 王棣台 <r04945002 at ntu.edu.tw> wrote:

> Hi, all
>
> I am the author of package "anamiR".
> I got a Warning message "Warning: dependency ''lumi" is not available"
> when I installed anamiR.
> Also, I tried other packages which depend on "lumi" package, and all got
> the same warning message.
> Is there any way I can solve this problem?
>
> Best regards,
> T.Wang
>
>
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