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           

Thanks in advance!

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