Thanks for the quick fix. No need to be sorry. /Henrik On Fri, Jan 30, 2015 at 9:36 AM, Michael Lawrence <lawrence.mich...@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 <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 > >
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel