[Bioc-devel] problem in building package GSAR
Rahmatallah, Yasir
YRahmatallah at uams.edu
Mon Aug 8 16:12:26 CEST 2016
Thank you Vincent and Wolfgang. With my limited knowledge of ‘subversion’, I overlooked this step. I think this will fix the problem.
Thank you very much.
Yasir
From: Vincent Carey [mailto:stvjc at channing.harvard.edu]
Sent: Monday, August 08, 2016 8:38 AM
To: Rahmatallah, Yasir
Cc: Wolfgang Huber; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] problem in building package GSAR
you have to do "svn add" for any new source files to be archived
On Mon, Aug 8, 2016 at 9:35 AM, Rahmatallah, Yasir <YRahmatallah at uams.edu<mailto:YRahmatallah at uams.edu>> wrote:
Dear Wolfgang,
I believe I did upload the source code (.R) of the new functions as well as their manual pages (.Rd).
First I checked out a copy of the development version using
svn co --username=y.rahmatallah --password=mypassword https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSAR<https://urldefense.proofpoint.com/v2/url?u=https-3A__hedgehog.fhcrc.org_bioconductor_trunk_madman_Rpacks_GSAR&d=AwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=lx5W6NJufGtK2Piccfk2o1lwPSqbwlJ_llxcnqLlPxY&s=tm_13HP_LE6GOytjpeaJYCkYBOfNZcj9_gZLegjOp_Y&e=>
I got the folder "GSAR" in the current directory. Then I added the source (.R) and manual page (.Rd) for each new function under the R and man folders respectively, modified the 'namespace' file by adding the new function names, and bumped the 3rd digit in the version field of the 'description' file and changed the 'Date' field too. When all this was done, I used
cd GSAR
svn update
svn commit --username=y.rahmatallah --password=mypassword -m "commit 1"
I always followed these steps in the past, but this is the first time I added new functions. Is there anything wrong in these steps?
Regards,
Yasir
-----Original Message-----
From: Wolfgang Huber [mailto:whuber at embl.de<mailto:whuber at embl.de>]
Sent: Saturday, August 06, 2016 4:39 AM
To: Rahmatallah, Yasir
Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] problem in building package GSAR
Dear Yasir
Did you actually upload the source code of these new function to the subversion server?
I get, right now
huber at boltzmann:~/madman/Rpacks/GSAR/R$ svn info .
…
URL: https://urldefense.proofpoint.com/v2/url?u=https-3A__hedgehog.fhcrc.org_bioconductor_trunk_madman_Rpacks_GSAR_R&d=AwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=jPnOxdZIGTe1L7i8CInlw-CbMQm_bUkUVqc5J0M5Bbw&s=YAk1b3miMlDYhwEUngUguZsC6-Q_iOJupf6-Wl9e-aI&e=
Revision: 119920
…
"grep AggrF *” in that directory does not yield any results.
"grep radial *” finds radial_ranking but not radial.ranking etc.
Wolfgang
> On Aug 6, 2016, at 0:34 GMT+2, Rahmatallah, Yasir <YRahmatallah at uams.edu<mailto:YRahmatallah at uams.edu>> wrote:
>
> Hi,
>
> I recently added 6 more functions to package GSAR. I added the R files
> and manual pages for the new functions. I updated the namespace file
> accordingly. I can build the package successfully on my windows PC and
> 'R CMD check' returns no errors or warnings. I can install the package
> and it works fine on my PC. I use svn to update the development
> version (current development version is 1.7.2). The last update
> returned the following error
>
> ** testing if installed package can be loaded Error in
> namespaceExport(ns, exports) :
> undefined exports: AggrFtest, radial.ranking, MDtest, RMDtest,
> findMST2.PPI, TestGeneSets
> Error: loading failed
>
> The undefined exports are the 6 new functions I added to the package. It's like they are declared in the namespace file but they don't exist elsewhere. Any idea what causes this error? Help is appreciated. The contents of the namespace file are shown below:
>
> export(
> AggrFtest,
> HDP.ranking,
> radial.ranking,
> WWtest,
> KStest,
> MDtest,
> RKStest,
> RMDtest,
> GSNCAtest,
> findMST2,
> findMST2.PPI,
> plotMST2.pathway,
> TestGeneSets
> )
>
> import(igraph)
> importFrom("stats", "cor", "dist", "sd", "var.test", "p.adjust")
> importFrom("graphics", "legend", "mtext", "par", "plot", "title")
>
> Thank you,
> Yasir
>
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Wolfgang
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany
wolfgang.huber at embl.de<mailto:wolfgang.huber at embl.de>
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