[Bioc-devel] elementNROWS vs elementLengths

[Hervé Pagès]

Hi,

On 03/03/2016 01:26 PM, Krithika Bhuvaneshwar wrote:
> Hi all,
>
> When I use the function elementLengths() in my the Bioc package that I
> am developing, the devtools::check() runs fine.
>
> Since elementLengths() is deprecated, I am now trying to use elementNROWS().

elementLengths() is deprecated in *Bioc-devel*.

>
> But when I try devtools::check() with elementNROWS(), it gives the
> following error:
>
> could not find function "elementNROWS"
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> I have updated my R version to 3.2.3, GenomicRanges latest version
> 1.22.4. Any idea why this would happen ? Attaching session info below.

You're using the current Bioc release. elementNROWS() was introduced in
Bioc-devel; there is no such function in Bioc release.

You should always use Bioc-devel when developing a new package. That's
because once accepted, your package will be added to Bioc-devel (which
will be released in April as BioC 3.3). The current Bioc-devel is based
on current R-devel (R 3.3), which will also be released in April. So
first install R-devel, then use biocLite() to install any Bioc-devel
package required by your package.

Cheers,
H.

>
> Thanks
> Krithika
>
>
>
>
>> sessionInfo()
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.9.5 (Mavericks)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.20.1 CINdex_0.99.7        BiocCheck_1.6.1
> GenomicRanges_1.22.4
> [5] GenomeInfoDb_1.6.3   IRanges_2.4.8        S4Vectors_0.8.11
> BiocGenerics_0.16.1
>
> loaded via a namespace (and not attached):
>   [1] Rcpp_0.12.3        XVector_0.10.0     bitops_1.0-6       tools_3.2.3
>   [5] zlibbioc_1.16.0    digest_0.6.9       memoise_1.0.0      gtable_0.2.0
>   [9] png_0.1-7          graph_1.48.0       DBI_0.3.1          gridExtra_2.2.1
> [13] httr_1.1.0         stringr_1.0.0      dplyr_0.4.3        knitr_1.12.3
> [17] gtools_3.5.0       caTools_1.17.1     devtools_1.10.0    grid_3.2.3
> [21] getopt_1.20.0      optparse_1.3.2     Biobase_2.30.0     R6_2.1.2
> [25] XML_3.98-1.4       RBGL_1.46.0        som_0.3-5          gdata_2.17.0
> [29] magrittr_1.5       gplots_2.17.0      codetools_0.2-14   biocViews_1.38.1
> [33] assertthat_0.1     RUnit_0.4.31       KernSmooth_2.23-15 stringi_1.0-1
> [37] RCurl_1.95-4.8
>
>> biocLite("BiocUpgrade")
> Error: Bioconductor version 3.2 cannot be upgraded with R version 3.2.3
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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