[Bioc-devel] I cannot reproduce the error my package raises in production

[Martin Morgan]

On 01/15/2018 03:31 AM, Carles Hernandez-Ferrer wrote:
> Dear all,
> 
> 
> During the package verification step I got the following error:
> 
> Quitting from lines 112-115 (batch_query.Rmd)
> Error: processing vignette 'batch_query.Rmd' failed with diagnostics:
> subscript out of bounds
> Execution halted
> 
> Unfortunately I cannot reproduce this error. I deployed the package in a
> PC with GNU/Linux, another PC with Windows and in all of them I am able
> to compile the three vignettes and the examples of the three main functions.
> 
>    * The last BioC check report:
>      https://bioconductor.org/spb_reports/CTDquerier_buildreport_20180115021154.html
>    * The issue on BioC contributions:
>      https://github.com/Bioconductor/Contributions/issues/588
>    * The package's GitHub page: https://github.com/isglobal-brge/CTDquerier
> 
> How can I try to find whats raising the "subscript out of bounds"?

Be sure to use the 'devel' version of Bioconductor for your package.

   http://bioconductor.org/developers/how-to/useDevel/

In this release cycle, this means using the devel version of R. Be sure 
your packages are up-to-date

   BiocInstaller::biocValid()

When I Stangle your vignette and source it

   cd CTDquerier/vignettes
   R CMD Stangle batch_query.Rmd
   R
   > source("batch_query.R", echo=TRUE)

the error reproduces at the line

 > xkr4 <- query_ctd_gene( terms = "XKR4" )
Error: subscript contains out-of-bounds indices
In addition: Warning messages:
1: In file(file, "rt") :
   cannot open file 'e65329a362d_CTD_genes.tsv.gz': No such file or 
directory
2: In query_ctd_gene(terms = "XKR4") : 1/1 terms were dropped.

Here's the traceback()

 > traceback()
12: stop(wmsg(...), call. = FALSE)
11: .subscript_error("subscript contains out-of-bounds indices")
10: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,
         allow.NAs = allow.NAs)
9: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,
        allow.NAs = allow.NAs)
8: normalizeSingleBracketSubscript(i, x, exact = FALSE, allow.NAs = TRUE,
        as.NSBS = TRUE)
7: extractROWS(x, i)
6: extractROWS(x, i)
5: keep[ii, 2]
4: keep[ii, 2]
3: stringr::str_replace(string = sel, pattern = "TERM", replacement = term)
2: get_ctd_url(index = "gene_gene_interaction", term = keep[ii,
        2], category = "gene")
1: query_ctd_gene(terms = "XKR4")

and I think the error is related to the warning message about file not 
found; likely it is on your local system, but not on the build system.

Martin


> 
> 
> Kind regards,
> C.
> 


This email message may contain legally privileged and/or...{{dropped:2}}