[Bioc-devel] spliceSites Vignette build error

[Dan Tenenbaum]

I can reproduce the error quite consistently by running either R CMD build or by sourcing the Stangled vignette.
Here is my sessionInfo after doing the latter. If you are running an older R devel please update it.

> sessionInfo()
R Under development (unstable) (2016-02-25 r70222)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] spliceSites_1.17.0  Biostrings_2.39.12  XVector_0.11.7
 [4] IRanges_2.5.39      S4Vectors_0.9.40    Biobase_2.31.3
 [7] BiocGenerics_0.17.3 refGenome_1.5.8     RSQLite_1.0.0
[10] DBI_0.3.1           doBy_4.5-14         survival_2.38-3
[13] rbamtools_2.14.3

loaded via a namespace (and not attached):
[1] lattice_0.20-33 MASS_7.3-45     grid_3.3.0      zlibbioc_1.17.0
[5] Matrix_1.2-4    splines_3.3.0   seqLogo_1.37.0
>

Dan


----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Wolfgang Kaisers" <Wolfgang.Kaisers at uni-duesseldorf.de>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, March 4, 2016 7:31:30 AM
> Subject: Re: [Bioc-devel] spliceSites Vignette build error

> Are you using R-devel on your computer?
> 
> ----- Original Message -----
>> From: "Wolfgang Kaisers" <Wolfgang.Kaisers at uni-duesseldorf.de>
>> To: "bioc-devel" <bioc-devel at r-project.org>
>> Sent: Friday, March 4, 2016 12:41:30 AM
>> Subject: [Bioc-devel] spliceSites Vignette build error
> 
>> Dear All,
>> 
>> the package check  on bioc-LATEST return an error during the vignette
>> build.
>> A broken dependency to another package of mine in CRAN seems to be the
>> reason.
>> 
>> The check using the last version available on CRAN is OK on my computer
>> and I added a dependency "refGenome (>= 1.5.8)" into the DESCRIPTION
>> file.
>> But the error is not resolved.
>> 
>> How shall I handle this?
>> 
>> Thanks
>> Wolfgang Kaisers
>> 
>> 
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - -#
>> The error in detail:
>> The build error message arises from the vignette 'spliceSites.Rnw':
>> Error: processing vignette 'spliceSites.Rnw' failed with diagnostics:
>>  chunk 34
>> Error in as.data.frame(y) :
>>   trying to get slot "ev" from an object (class "data.frame") that is
>> not an S4 object
>> 
>> The error is thrown by the function 'uniqueJuncAnn' (in line 294 chunk
>> 34 spliceSites.Rnw).
>> Inside uniqueJuncAnn, there are two data.frames merged (in line 3386 of
>> spliceSites.r).
>> The right-hand object (uj at ev$gtf) refers to a 'refJunctions' object
>> which is defined
>> in my CRAN package refGenome.
>> 
>> I recently changed the type of this object (which is present on CRAN
>> since July 2015).
>> 
>> _______________________________________________
>> 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