Can't make working link in roxygen2
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Entering edit mode
b.nota ▴ 360
@bnota-7379
Last seen 2.2 years ago
Netherlands

Hello,

I know that roxygen2 is not part of bioconductor, but since I am using it in combination with bioconductor packages I thought I make a chance here to find an answer.

I am using roxygen2 to document my R package in development, and if I want to refer in the help manual to certain functions in other packages, I don't get the link in the HTML page which is generated.

For example, if I want to refer to the goseq function in the goseq package, I type:

#' @param x An object containing the data frame generated with \code{\link[goseq]{goseq}} function.

But it won't appear as a link in my help HTML page. Does anyone has an idea why it doesn't work for me? It seems also not to work when I refer to other functions in my own package:

#' @param x An object containing the data frame created with \code{\link{my.other.function}} function.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] functions1_0.0.0.9000 gplots_2.17.0         devtools_1.11.1
[4] limma_3.24.15         goseq_1.20.0          RSQLite_1.0.0
[7] DBI_0.3.1             geneLenDataBase_1.4.0 BiasedUrn_1.07
[10] roxygen2_5.0.1.9000

loaded via a namespace (and not attached):
[1] gtools_3.5.0            lattice_0.20-33         stats4_3.2.2
[4] rtracklayer_1.28.10     mgcv_1.8-11             GenomicFeatures_1.20.6
[7] XML_3.98-1.3            withr_1.0.1             BiocParallel_1.2.22
[10] BiocGenerics_0.14.0     lambda.r_1.1.7          stringr_1.0.0
[13] zlibbioc_1.14.0         Biostrings_2.36.4       futile.logger_1.4.1
[16] caTools_1.17.1          memoise_1.0.0           Biobase_2.28.0
[19] IRanges_2.2.9           biomaRt_2.24.1          GenomeInfoDb_1.4.3
[22] parallel_3.2.2          AnnotationDbi_1.30.1    Rcpp_0.12.4
[25] KernSmooth_2.23-15      gdata_2.17.0            S4Vectors_0.6.6
[28] XVector_0.8.0           Rsamtools_1.20.5        digest_0.6.9
[31] stringi_1.0-1           GenomicRanges_1.20.8    grid_3.2.2
[34] tools_3.2.2             bitops_1.0-6            magrittr_1.5
[37] RCurl_1.95-4.7          futile.options_1.0.0    GO.db_3.1.2
[40] whisker_0.3-2           Matrix_1.2-3            rstudioapi_0.5
[43] GenomicAlignments_1.4.2 nlme_3.1-124


roxygen2 • 2.5k views
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Entering edit mode

Remember to use the development version of Bioconductor when developing packages.  It might help to also include the commands you use to build and install your package.  Maybe your package is on github so you can share a link to your problem?

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Yeah you're right, will try to finish it with the development version of bioc. It's not on github yet, I am still writing the documents and manual...

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@steve-lianoglou-2771
Last seen 3 months ago
United States

It should work, but perhaps it doesn't work until you install the package and use it after you load it via a library call, as opposed to using the package (and therefore viewing the docs) in "devmode" ie. using the package after you load it via devtools::load_all

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Entering edit mode

Ah, thanks! I will try to install it when I am done documenting...

Strange thing now is that a hyperlink does work in devmode.