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.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
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