Message-ID: <CAFDcVCTZ+NTMLrqQw9_6fbeTY-HULAQ8_cubTtnCfDA=gem8Bg@mail.gmail.com>
Date: 2015-01-30T18:11:20Z
From: Henrik Bengtsson
Subject: [Bioc-devel] BiocGenerics fails to install from source on R-devel (aka "there is no package called '2015-01-30 09:23:26'")
In-Reply-To: <CAOQ5Nyc37w=A6gpE4ONvVU9EL9uh3ut610nSviQJLHUvX2Z0qw@mail.gmail.com>
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 ?BiocGenerics? ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Creating a new generic function for ?append? in package ?BiocGenerics?
>> Creating a new generic function for ?as.data.frame? in package
>> ?BiocGenerics?
>> Creating a new generic function for ?as.vector? in package ?BiocGenerics?
>> Creating a new generic function for ?cbind? in package ?BiocGenerics?
>> Creating a new generic function for ?rbind? in package ?BiocGenerics?
>> Creating a new generic function for ?do.call? in package ?BiocGenerics?
>> Creating a new generic function for ?duplicated? in package ?BiocGenerics?
>> Creating a new generic function for ?anyDuplicated? in package
>> ?BiocGenerics?
>> Creating a new generic function for ?eval? in package ?BiocGenerics?
>> Creating a new generic function for ?pmax? in package ?BiocGenerics?
>> Creating a new generic function for ?pmin? in package ?BiocGenerics?
>> Creating a new generic function for ?pmax.int? in package ?BiocGenerics?
>> Creating a new generic function for ?pmin.int? in package ?BiocGenerics?
>> Creating a new generic function for ?Reduce? in package ?BiocGenerics?
>> Creating a new generic function for ?Filter? in package ?BiocGenerics?
>> Creating a new generic function for ?Find? in package ?BiocGenerics?
>> Creating a new generic function for ?Map? in package ?BiocGenerics?
>> Creating a new generic function for ?Position? in package ?BiocGenerics?
>> Creating a new generic function for ?get? in package ?BiocGenerics?
>> Creating a new generic function for ?mget? in package ?BiocGenerics?
>> Creating a new generic function for ?is.unsorted? in package
>> ?BiocGenerics?
>> Creating a new generic function for ?lapply? in package ?BiocGenerics?
>> Creating a new generic function for ?sapply? in package ?BiocGenerics?
>> Creating a new generic function for ?mapply? in package ?BiocGenerics?
>> Creating a new generic function for ?match? in package ?BiocGenerics?
>> Creating a new generic function for ?order? in package ?BiocGenerics?
>> Creating a new generic function for ?paste? in package ?BiocGenerics?
>> Creating a new generic function for ?rank? in package ?BiocGenerics?
>> Creating a new generic function for ?rep.int? in package ?BiocGenerics?
>> Creating a new generic function for ?rownames? in package ?BiocGenerics?
>> Creating a new generic function for ?colnames? in package ?BiocGenerics?
>> Creating a new generic function for ?union? in package ?BiocGenerics?
>> Creating a new generic function for ?intersect? in package ?BiocGenerics?
>> Creating a new generic function for ?setdiff? in package ?BiocGenerics?
>> Creating a new generic function for ?sort? in package ?BiocGenerics?
>> Creating a new generic function for ?table? in package ?BiocGenerics?
>> Creating a new generic function for ?tapply? in package ?BiocGenerics?
>> Creating a new generic function for ?unique? in package ?BiocGenerics?
>> Creating a new generic function for ?unlist? in package ?BiocGenerics?
>> Creating a new generic function for ?unsplit? in package ?BiocGenerics?
>> Creating a new generic function for ?xtabs? in package ?BiocGenerics?
>> Creating a new generic function for ?clusterCall? in package
>> ?BiocGenerics?
>> Creating a new generic function for ?clusterApply? in package
>> ?BiocGenerics?
>> Creating a new generic function for ?clusterApplyLB? in package
>> ?BiocGenerics?
>> Creating a new generic function for ?clusterEvalQ? in package
>> ?BiocGenerics?
>> Warning in getPackageName(environment(fdef)) :
>> Created a package name, ?2015-01-30 09:28:06?, when none found
>> Error in loadNamespace(name) :
>> there is no package called ?2015-01-30 09:28:06?
>> Error : unable to load R code in package ?BiocGenerics?
>> ERROR: lazy loading failed for package ?BiocGenerics?
>> * removing
>> ?/compbio/henrik/R/x86_64-unknown-linux-gnu-library/3.2/BiocGenerics?
>> * restoring previous
>> ?/compbio/henrik/R/x86_64-unknown-linux-gnu-library/3.2/BiocGenerics?
>>
>>
>> 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, ?2015-01-30 09:06:54?, 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
>
>