[Bioc-devel] problem in building package GSAR

[Vincent Carey]

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>
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
>
> 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]
> Sent: Saturday, August 06, 2016 4:39 AM
> To: Rahmatallah, Yasir
> Cc: 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>
> 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
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>
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