Just checked in the fix to R-devel. No more error, and the warning is also
fixed.
Sorry,
Michael
On Fri, Jan 30, 2015 at 9:29 AM, Henrik Bengtsson <h...@biostat.ucsf.edu>
wrote:
> I'm posting to bioc-devel, but I suspect it would end up on R-devel.
> Feel free to continue the thread there at any time.
>
>
> PROBLEM:
> $ Rscript --vanilla -e
> "source('http://bioconductor.org/biocLite.R');biocLite('BiocGenerics',
> type='source')"
>
> Bioconductor version 3.1 (BiocInstaller 1.17.5), ?biocLite for help
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.1 (BiocInstaller 1.17.5), R version 3.2.0.
> Installing package(s) 'BiocGenerics'
> trying URL '
> http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocGenerics_0.13.4.tar.gz
> '
> Content type 'application/x-gzip' length 34031 bytes (33 KB)
> opened URL
> ==================================================
> downloaded 33 KB
>
> * installing *source* package âBiocGenericsâ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Creating a new generic function for âappendâ in package âBiocGenericsâ
> Creating a new generic function for âas.data.frameâ in package
> âBiocGenericsâ
> Creating a new generic function for âas.vectorâ in package âBiocGenericsâ
> Creating a new generic function for âcbindâ in package âBiocGenericsâ
> Creating a new generic function for ârbindâ in package âBiocGenericsâ
> Creating a new generic function for âdo.callâ in package âBiocGenericsâ
> Creating a new generic function for âduplicatedâ in package âBiocGenericsâ
> Creating a new generic function for âanyDuplicatedâ in package
> âBiocGenericsâ
> Creating a new generic function for âevalâ in package âBiocGenericsâ
> Creating a new generic function for âpmaxâ in package âBiocGenericsâ
> Creating a new generic function for âpminâ in package âBiocGenericsâ
> Creating a new generic function for âpmax.intâ in package âBiocGenericsâ
> Creating a new generic function for âpmin.intâ in package âBiocGenericsâ
> Creating a new generic function for âReduceâ in package âBiocGenericsâ
> Creating a new generic function for âFilterâ in package âBiocGenericsâ
> Creating a new generic function for âFindâ in package âBiocGenericsâ
> Creating a new generic function for âMapâ in package âBiocGenericsâ
> Creating a new generic function for âPositionâ in package âBiocGenericsâ
> Creating a new generic function for âgetâ in package âBiocGenericsâ
> Creating a new generic function for âmgetâ in package âBiocGenericsâ
> Creating a new generic function for âis.unsortedâ in package âBiocGenericsâ
> Creating a new generic function for âlapplyâ in package âBiocGenericsâ
> Creating a new generic function for âsapplyâ in package âBiocGenericsâ
> Creating a new generic function for âmapplyâ in package âBiocGenericsâ
> Creating a new generic function for âmatchâ in package âBiocGenericsâ
> Creating a new generic function for âorderâ in package âBiocGenericsâ
> Creating a new generic function for âpasteâ in package âBiocGenericsâ
> Creating a new generic function for ârankâ in package âBiocGenericsâ
> Creating a new generic function for ârep.intâ in package âBiocGenericsâ
> Creating a new generic function for ârownamesâ in package âBiocGenericsâ
> Creating a new generic function for âcolnamesâ in package âBiocGenericsâ
> Creating a new generic function for âunionâ in package âBiocGenericsâ
> Creating a new generic function for âintersectâ in package âBiocGenericsâ
> Creating a new generic function for âsetdiffâ in package âBiocGenericsâ
> Creating a new generic function for âsortâ in package âBiocGenericsâ
> Creating a new generic function for âtableâ in package âBiocGenericsâ
> Creating a new generic function for âtapplyâ in package âBiocGenericsâ
> Creating a new generic function for âuniqueâ in package âBiocGenericsâ
> Creating a new generic function for âunlistâ in package âBiocGenericsâ
> Creating a new generic function for âunsplitâ in package âBiocGenericsâ
> Creating a new generic function for âxtabsâ in package âBiocGenericsâ
> Creating a new generic function for âclusterCallâ in package âBiocGenericsâ
> Creating a new generic function for âclusterApplyâ in package
> âBiocGenericsâ
> Creating a new generic function for âclusterApplyLBâ in package
> âBiocGenericsâ
> Creating a new generic function for âclusterEvalQâ in package
> âBiocGenericsâ
> Warning in getPackageName(environment(fdef)) :
> Created a package name, â2015-01-30 09:28:06â, when none found
> Error in loadNamespace(name) :
> there is no package called â2015-01-30 09:28:06â
> Error : unable to load R code in package âBiocGenericsâ
> ERROR: lazy loading failed for package âBiocGenericsâ
> * removing
> â/compbio/henrik/R/x86_64-unknown-linux-gnu-library/3.2/BiocGenericsâ
> * restoring previous
> â/compbio/henrik/R/x86_64-unknown-linux-gnu-library/3.2/BiocGenericsâ
>
>
> I can reproduce this on R-devel (2015-01-30 r67664) on both Linux and
> Windows (haven't checked OS X).
>
> $ R --version
> R Under development (unstable) (2015-01-30 r67664) -- "Unsuffered
> Consequences"
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> $ R --version
> R Under development (unstable) (2015-01-30 r67664) -- "Unsuffered
> Consequences"
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> I also get this with a minimal Travis CI Ubuntu setup on R-devel
> [https://travis-ci.org/HenrikBengtsson/issue-BiocGenerics/builds/48918063
> ].
>
>
> SOME TROUBLESHOOTING:
> Not sure if the failure is related to:
>
> Warning in getPackageName(environment(fdef)) :
> Created a package name, â2015-01-30 09:06:54â, when none found
>
> but it occurs immediately after this. I've seen this warning
> previously and it appears on all OSes as well, but does not cause the
> package installation to fail, cf.
> http://master.bioconductor.org/checkResults/devel/bioc-LATEST/BiocGenerics/
> .
> BTW, it's not the first time that "timestamp-as-package name" warning
> shows up:
>
> https://stat.ethz.ch/pipermail/r-devel/2013-December/068113.html
> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15481
>
> That was related to S4. I had the impression it was resolved, but
> then I also haven't followed it closely.
>
> /Henrik
> Bug Whisperer
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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