[Bioc-devel] Adding NAMESPACE file to packages (redux)

[Patrick Aboyoun]

Bioconductor package maintainers,
This is a reissue of a message sent out earlier in the BioC 2.4 
development cycle to remind those who haven't had time to add a 
NAMESPACE file to your package to please do so before the release. As 
Nishant pointed out below, namespaces help to ensure that your packages 
use functions you intended them to use and export functions you expect 
end users to have access to. For example, the IRanges and Biobase 
packages both have generic methods for annotation and, setting aside the 
design decision for this name conflict, this causes a handful of 
packages to break because the wrong annotation generic is being chosen 
during code execution. By importing the appropriate generic into your 
package's namespace, you can avoid these types of issues.

There are currently 64 packages in the BioC 2.4 code line without 
NAMESPACE files. If you or someone you collaborate with maintain one of 
the following packages, please add the missing NAMESPACE files to help 
lock down the packages so as to avoid issues like the one mentioned 
above in the future:

 [1] "ABarray"            "aCGH"               "affypdnn"         
 [4] "affyQCReport"       "annotationTools"    "apComplex"        
 [7] "CALIB"              "convert"            "CORREP"           
[10] "daMA"               "DEDS"               "diffGeneAnalysis" 
[13] "EBarrays"           "ecolitk"            "factDesign"       
[16] "fdrame"             "genArise"           "geneRecommender"  
[19] "GeneSpring"         "GeneTraffic"        "GLAD"             
[22] "goTools"            "GraphAT"            "Harshlight"       
[25] "Heatplus"           "HEM"                "iterativeBMAsurv" 
[28] "keggorth"           "lapmix"             "LBE"              
[31] "limmaGUI"           "LMGene"             "LPE"              
[34] "maanova"            "maCorrPlot"         "made4"            
[37] "makePlatformDesign" "MantelCorr"         "maSigPro"         
[40] "minet"              "MiPP"               "nudge"            
[43] "OCplus"             "OrderedList"        "panp"             
[46] "pickgene"           "plier"              "qvalue"           
[49] "RankProd"           "RbcBook1"           "RLMM"             
[52] "RMAGEML"            "rsbml"              "safe"             
[55] "sagenhaft"          "SLqPCR"             "spikeLI"          
[58] "sscore"             "ssize"              "stepNorm"         
[61] "timecourse"         "twilight"           "weaver"           
[64] "webbioc"          


As mentioned in the previous e-mail, you can learn more about NAMESPACE 
files in section 1.6 of the "Writing R Extensions"manual at the CRAN 
website:

    http://cran.r-project.org/doc/manuals/R-exts.html#Package-name-spaces

There is also an RNEWS article (#54) by Luke Tierney regarding NAMESPACEs at
    
    http://cran.r-project.org/doc/Rnews/Rnews_2003-1.pdf

as well as some helpful hints in Robert Gentleman's book.

    http://www.bioconductor.org/pub/RBioinf/


Thanks,
Patrick


Nishant Gopalakrishnan wrote:
>     Dear Bioconductor developers,
>
>     We have noticed that several packages in the Bioconductor repository
> do not
>     have a NAMESPACE file.
>
>     In the interest of reducing the number of objects on the search
> path, we are
>     requesting that all the Bioconductor developers add a NAMESPACE file
> to their
>     package at this time.
>     
>     Adding a namespace offers several advantages
>
>     1) It lets other packages import functions but not put the package
> on the
>     search path.
>
>     2) It helps ensure that your functions always work as intended since
> you
>     have control over which functions are used in your package, even if
>     identically named ones are introduced in other packages.
>
>     3) It simplifies the user interface so that only the important
> functions are
>     exposed while allowing the private functions to be available for
> internal use.
>
>     
>     For general information regarding the process of adding a NAMESPACE
> to your
>     package, please refer to section 1.6 of the "Writing R Extensions"
> manual at
>     the CRAN website.
>
>     http://cran.r-project.org/doc/manuals/R-exts.html#Package-name-spaces
>
>     There is also a great RNEWS article (#54) by Luke Tierney regarding
>     NAMESPACEs.
>     
>     http://cran.r-project.org/doc/Rnews/Rnews_2003-1.pdf
>
>     You might also find some helpful hints in Roberts book.
>
>     http://www.bioconductor.org/pub/RBioinf/
>
>  
>     If you have additional questions, please contact us by posting to the
>     bioc-devel mailing list.  We will be glad to help.
>
>
>     Thanks in advance for your time and effort,
>
>
>     The Bioconductor core team
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>