Question: Weird error in the package submission
0
gravatar for alper.kucukural
3.8 years ago by
UMass Medical School Worcester MA
alper.kucukural10 wrote:

Hi,

When I am submitting a package, I got just one error that I couldn't solve it. It is working on many different machines but not on builders. 

I am using a function called enrichGO from another bioconductor package from clusterProfiler. It is saying unused argument but, that function is actually using it. 

Error in enrichGO(gene = genelist, organism = org, ont = ont, pvalueCutoff = pvalueCutoff,  : unused argument (organism = org)

How can we fix this? The issue# is 1408.

Thanks,

Alper

software error • 937 views
ADD COMMENTlink modified 3.8 years ago by Dan Tenenbaum8.2k • written 3.8 years ago by alper.kucukural10

Simply specify the OrgDb that will solve your issue.

E.g.
OrgDb='org.Hs.eg.db'

 

ADD REPLYlink written 2.3 years ago by Kolin Harinda Rajapaksha0
Answer: Weird error in the package submission
0
gravatar for Martin Morgan
3.8 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

From the clusterProfiler Bioconductor github mirror you can see that the development version of the package does not have 'organism' in its argument list, so in your code (function getEnrichGO, for instance) you are not allowed to use the argument. Maybe you are developing your code using Bioc-release and R-3.2.3, rather than Bioc-devel and R-devel?

Questions about package development should be directed to the Bioconductor developer mailing list.

ADD COMMENTlink written 3.8 years ago by Martin Morgan ♦♦ 24k
Answer: Weird error in the package submission
0
gravatar for Dan Tenenbaum
3.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

Questions about packages you are submitting should go to bioc-devel.

But the answer is, you need to be using R-devel when you develop your package, because the next release of Bioconductor will only work with that version (which will be called R-3.3 upon its release).

The clusterProfiler package has changed between release and devel. In release, its arguments are:

> args(enrichGO)
function (gene, organism = "human", ont = "MF", pvalueCutoff = 0.05,
    pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 5,
    readable = FALSE)

In devel they are:

> args(enrichGO)
function (gene, OrgDb, keytype = "ENTREZID", ont = "MF", pvalueCutoff = 0.05,
    pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 5,
    readable = FALSE)

?enrichGO provides further information. Note that in release the organism argument is meant to be a character vector and in devel it appears this argument (no longer named, but required) is supposed to be an OrgDb object. clusterProfiler's NEWS file may also be helpful.

 

ADD COMMENTlink written 3.8 years ago by Dan Tenenbaum8.2k
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