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

4 messages · Michael Lawrence, Henrik Bengtsson, Martin Morgan

Original
Henrik Bengtsson
# 
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
Michael Lawrence
# 
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:

  
  


  


      

    

    

      
      

        


  

        

      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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
      #
    

  


  

      
On 01/30/2015 10:11 AM, Henrik Bengtsson wrote:

            

      
      
      
    

        
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