Dear Bioconductors,

I'm using GOstats for computing over-representation of GO terms based on a list of entrezIDs. As final step, I'm generating an html report using htmlReport() on the resulting "GOHyperGResult" object.

params <- new("GOHyperGParams",
              geneIds=as.character(selectedEntrezIDs),
              universeGeneIds=as.character(entrezUniverse),
              annotation="hgu133a.db",
              ontology="BP",
              pvalueCutoff=0.001,
              conditional=FALSE,
              testDirection="over")
hgOver <- hyperGTest(params)
htmlReport(hgOver, file="GOhtml.html",summary.args=list("htmlLinks"=TRUE))

My question now is related to the URL-links as provided in the "Term" column of the html report file:

the URL behind each hyperlink points to "www.godatabase.org" but this webseite seems to be offline.

ping www.godatabase.org
PING godatabase.org (54.83.197.87) 56(84) bytes of data.
^C
--- godatabase.org ping statistics ---
7 packets transmitted, 0 received, 100% packet loss, time 6047ms

As clarification, I take "GO:2001252" as example: The URL as assembled by htmlReport() is

http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:2001252

but this directly goes to dev/null (= no connection established)

As an alternative, this link would work: http://amigo.geneontology.org/amigo/term/GO:2001252

As the URL-snipped to www.godatabase.org is hard-coded in

/R/hyperGtable.R:94:              AMIGO_URL <- "http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=%s"

As I'm just a beginner with GOstats, so I do not know if the hyperlinks used to work in the past, hence if it is currently a problem on the www.godatabase.org side or not.

Many thanks for any help.

Christian

####################

sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] GOstats_2.38.0       graph_1.50.0         Category_2.38.0     
[4] Matrix_1.2-6         AnnotationDbi_1.34.0 IRanges_2.6.0       
[7] S4Vectors_0.10.0     Biobase_2.32.0       BiocGenerics_0.18.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-33        GO.db_3.3.0            XML_3.98-1.4          
 [4] AnnotationForge_1.14.0 RBGL_1.48.0            grid_3.3.0            
 [7] xtable_1.8-2           DBI_0.4                GSEABase_1.34.0       
[10] RSQLite_1.0.0          genefilter_1.54.0      annotate_1.50.0       
[13] splines_3.3.0          survival_2.39-2       

Thanks for the bug report. Fixed in both release and devel; these should propagate through the build servers and be available to biocLite in a day or two.

Dear James,

thanks for your quick reply :-)

Regards

Christian