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
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