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

Martin Morgan mtmorgan at fredhutch.org
Fri Jan 30 19:20:14 CET 2015


On 01/30/2015 10:11 AM, Henrik Bengtsson wrote:
> Thanks for the quick fix. No need to be sorry. /Henrik

especially since the cumulative changes in R-devel are starting to make a pretty 
reasonable difference to load times (and presumably other aspects) of S4-heavy 
packages! Thanks Michael & Pete Haverty

Martin

>
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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