[Bioc-devel] problem in building package GSAR

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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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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a...{{dropped:10}}

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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
huber.embl.de&d=AwIFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-
Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=jPnOxdZIGTe1L7i8CInlw-CbMQm_
bUkUVqc5J0M5Bbw&s=QxkP6_zFY3S0j-pTnzvF_vp3CuNbxUlBhczHD32U_OM&e=










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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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