[Bioc-devel] problem in building package GSAR

[Rahmatallah, Yasir]

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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Re: [Bioc-devel] Imports version that's only available on github?

[Martin Morgan]

On 08/05/2016 01:55 PM, Alex Pickering wrote:

My package requires a version of 'DT' that's only available on github. I
tried following the answer to this SO

(specifying 'Remotes' in the DESCRIPTION in addition to the version needed
in 'Imports'). Build failed with "Package required and available but
unsuitable version: 'DT'". How should this be handled? Thank you,


Packages must be on CRAN or Bioconductor; the rationale is that these 
represent stable, tested, and somehow mature packages, rather than an 
arbitrary package of unknown stability. The StackOverflow question is a 
solution for devtools, but biocLite() uses install.packages().


Martin



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[Bioc-devel] Imports version that's only available on github?

[Alex Pickering]

My package requires a version of 'DT' that's only available on github. I
tried following the answer to this SO

(specifying 'Remotes' in the DESCRIPTION in addition to the version needed
in 'Imports'). Build failed with "Package required and available but
unsuitable version: 'DT'". How should this be handled? Thank you,

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Re: [Bioc-devel] failing to build on moscato2

[Martin Morgan]

On 08/05/2016 04:40 AM, Ludwig Geistlinger wrote:

Hi,

according to

http://bioconductor.org/checkResults/release/bioc-LATEST/EnrichmentBrowser/moscato2-buildsrc.html

my package is failing to build due to

ERROR: dependencies 'Biobase', 'S4Vectors', 'graph', 'limma' are not
available for package 'EnrichmentBrowser'

However, these dependencies seems to have built without problems.
What is the problem here?


The build report you link to is from earlier in the week, where builds 
failed because of


  https://stat.ethz.ch/pipermail/bioc-devel/2016-July/009566.html

Your package isn't included in the most recent build report because the 
DESCRIPTION file is malformed:


RELEASE_3_3/madman/Rpacks/EnrichmentBrowser$ R --vanilla CMD INSTALL .
* installing to library 
‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3-Bioc-3.4’

ERROR: no 'Package' field in 'DESCRIPTION'

Martin



Thanks,
Ludwig






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[Bioc-devel] failing to build on moscato2

[Ludwig Geistlinger]

Hi,

according to

http://bioconductor.org/checkResults/release/bioc-LATEST/EnrichmentBrowser/moscato2-buildsrc.html

my package is failing to build due to

ERROR: dependencies 'Biobase', 'S4Vectors', 'graph', 'limma' are not
available for package 'EnrichmentBrowser'

However, these dependencies seems to have built without problems.
What is the problem here?

Thanks,
Ludwig



-- 
Dr. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de

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