[Bioc-devel] BiocGenerics fails to install from source on R-devel (aka "there is no package called '2015-01-30 09:23:26'")

[Henrik Bengtsson]

Thanks for the quick fix. No need to be sorry. /Henrik

On Fri, Jan 30, 2015 at 9:36 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> 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 <hb at 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
>>
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>
>