I am trying to use makePDpackage for the Affymetrix Arabidopsis Tiling array. I ran the following code with no errors: library(makePlatformDesign) makePDpackage("At35b_MR_v04-2_TIGRv5.bpmap",file1="At35b_MR_v04.cif",m anufacturer="affymetrix",type="tiling") The (after exiting R), I ran the following command: R CMD check pd.at35b.mr.v04.2.tigrv5 At this point, I got 4 warnings (excerpted): * checking for unstated dependencies in R code ... WARNING 'library' or 'require' calls not declared from: oligo * checking for missing documentation entries ... WARNING Undocumented code objects: pd.at35b.mr.v04.2.tigrv5 Undocumented data sets: pd.at35b.mr.v04.2.tigrv5 * checking for code/documentation mismatches ... WARNING Error in tools::codoc(package = "pd.at35b.mr.v04.2.tigrv5") : directory '/home/hess/Tiling/CELfiles/pd.at35b.mr.v04.2.tigrv5.Rcheck/pd.at35b.m r.v04.2.tigrv5' does not contain Rd sources Execution halted * checking Rd \usage sections ... WARNING Error in tools::checkDocFiles(package = "pd.at35b.mr.v04.2.tigrv5") : directory '/home/hess/Tiling/CELfiles/pd.at35b.mr.v04.2.tigrv5.Rcheck/pd.at35b.m r.v04.2.tigrv5' does not contain Rd sources Execution halted Just to see what would happen, I also tried: R CMD build pd.at35b.mr.v04.2.tigrv5 and got the following warning: * checking for empty or unneeded directories WARNING: directory 'pd.at35b.mr.v04.2.tigrv5/man' is empty I get an error when I try to load the package in R: > library(pd.at35b.mr.v04.2.tigrv5) Error in library(pd.at35b.mr.v04.2.tigrv5) : 'pd.at35b.mr.v04.2.tigrv5' is not a valid package -- installed < 2.0.0? I am working in R version 2.6.0 with makePlatformDesign_1.2.0 on linux redhat. I would like to figure out where I have gone wrong before repeating, because it takes several hours to run! Any suggestions would be appreciated. Ann

Hi Ann, Ann Hess wrote: > I am trying to use makePDpackage for the Affymetrix Arabidopsis Tiling > array. I ran the following code with no errors: > > library(makePlatformDesign) > makePDpackage("At35b_MR_v04-2_TIGRv5.bpmap",file1="At35b_MR_v04.cif" ,manufacturer="affymetrix",type="tiling") > > > The (after exiting R), I ran the following command: > R CMD check pd.at35b.mr.v04.2.tigrv5 > > At this point, I got 4 warnings (excerpted): > > * checking for unstated dependencies in R code ... WARNING > 'library' or 'require' calls not declared from: > oligo > * checking for missing documentation entries ... WARNING > Undocumented code objects: > pd.at35b.mr.v04.2.tigrv5 > Undocumented data sets: > pd.at35b.mr.v04.2.tigrv5 > * checking for code/documentation mismatches ... WARNING > Error in tools::codoc(package = "pd.at35b.mr.v04.2.tigrv5") : > directory > '/home/hess/Tiling/CELfiles/pd.at35b.mr.v04.2.tigrv5.Rcheck/pd.at35b .mr.v04.2.tigrv5' > does not contain Rd sources > Execution halted > * checking Rd \usage sections ... WARNING > Error in tools::checkDocFiles(package = "pd.at35b.mr.v04.2.tigrv5") : > directory > '/home/hess/Tiling/CELfiles/pd.at35b.mr.v04.2.tigrv5.Rcheck/pd.at35b .mr.v04.2.tigrv5' > does not contain Rd sources > Execution halted Yes. The pDPackage won't have any .Rd files, so checking for these things and for code/documentation mismatches won't work. Try R CMD check --no-codoc pd.at35b.mr.v04.2.tigrv5 You might also need to add some other options - see R CMD check --help. > > Just to see what would happen, I also tried: > R CMD build pd.at35b.mr.v04.2.tigrv5 > > and got the following warning: > * checking for empty or unneeded directories > WARNING: directory 'pd.at35b.mr.v04.2.tigrv5/man' is empty > > I get an error when I try to load the package in R: > >> library(pd.at35b.mr.v04.2.tigrv5) > Error in library(pd.at35b.mr.v04.2.tigrv5) : > 'pd.at35b.mr.v04.2.tigrv5' is not a valid package -- installed < 2.0.0? This error usually happens when people take package sources and dump them in the library folder. If you did something like that, then there's your answer. If not then I dunno. Do note that you need to *install* the package and building does not do that. Also note that you don't need to build before installing. The canonical way to do things is R CMD check <thepackage> R CMD build <thepackage> R CMD INSTALL <thepackage_version.tar.gz> but if you just want the thing installed you can skip all that stuff and just do R CMD INSTALL <thepackage> And one last thing. It's my understanding that makePlatformDesign is on its way out, to be replaced by pdInfoBuilder. This is a bit more complicated as you will need to first set up a PDInfoPkgSeed object. The man page is not clear at all about how to do this, but you will need the bpmap and cif file (from the Affy website - it should be in the library file) and to do something along these lines: pkg <- new("AffyTilingPDInfoPkgSeed", bpmapFile=<the bpmapfile="">, cifFile = <the ciffile="">, version = "0.0.1", author = "Ann Hess", email = "hess at stat.colostate.edu", genomeBuild = "um, I dunno", biocViews = "annotationData") makePDInfoPackage(pkg) Then install as usual. Best, Jim > > I am working in R version 2.6.0 with makePlatformDesign_1.2.0 on linux > redhat. > > I would like to figure out where I have gone wrong before repeating, > because it takes several hours to run! > > Any suggestions would be appreciated. > > Ann > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623