On 03/03/2011 06:47 AM, Robert M. Flight wrote: > Hi Martin, > > Thanks for that. I knew it would be hard to spot what was going on > without having a reproducible example that did not depend on the > functions in the package I'm developing. I spent a day hunting down > the bug and figuring out a way to reproduce my problem. Originally it > was extremely confusing because the example was running a wrapper > function that uses the one that was failing, making it a pain in the > butt to figure out just what it was that was going wrong. And running > the examples independently worked too. It was only running them > sequentially following cleanEx() that things start to go haywire. yes; if you R CMD check pkg then look in pkg.Rcheck you'll see foo- Ex.R and foo-Ex.Rout; these can be helpful for tracking down these issues, e.g., R -f foo-Ex.R. I trimmed your example to pkgname <- "FOO" source(file.path(R.home("share"), "R", "examples-header.R")) library('Category') assign(".oldSearch", search(), pos = 'CheckExEnv') cleanEx() nameEx("Ex1") datPkg <- DatPkgFactory('org.Hs.eg.db') ID2EntrezID(datPkg) cleanEx() nameEx("Ex2") datPkg <- DatPkgFactory('org.Hs.eg.db') ID2EntrezID(datPkg) before digging in to the details. Martin > > -Robert > > On Thu, Mar 3, 2011 at 09:33, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> On 03/03/2011 06:21 AM, Sean Davis wrote: >>> On Thu, Mar 3, 2011 at 8:47 AM, Robert M. Flight <rflight79 at="" gmail.com="">wrote: >>> >>>> Hi All, >>>> >>>> I am developing a package that depends on Category. As part of my >>>> package development, I decided that I should use R CMD check and >>>> documentation examples to verify that my functions are working >>>> properly. Unfortunately, it appears that after the "cleanEx()" >>>> function removes certain packages that are used to access annotation >>>> packages (DBI and RSQLITE), they don't get reloaded again for the next >>>> example, even though it consists of very similar code. I have a toy >>>> example below that fails in exactly the same way that my actual >>>> examples do. >>>> >>>> >From what I can tell using search(), the important package that is not >>>> getting reloaded is "DBI". Should I simply include that in the >>>> "library" call in my examples, or is this something that should be >>>> fixed somewhere else? >>>> >>>> >>> The examples are meant to be independent of each other, so loading a package >>> in one example does not mean it is loaded in another example. >>> >>> There are a few ways to deal with this: >>> >>> 1) Use library() in every example. You may want to fail gracefully by >>> using require() and an if statement. You will want to consider adding the >>> required packages to "suggests" in DESCRIPTION. >>> 2) Label the examples as doNotRun. The downside is that you don't get >>> example checking, obviously. >>> 3) Add the required Imports to the NAMESPACE and DESCRIPTION files. >>> >>> These types of questions are probably best asked on the bioc-devel list, so >>> if you have further questions, you could start a new thread there. >> >> Actually, I think there's a NAMESPACE problem with annotate; it should >> Import: DBI and importMethodsFrom(DBI, dbGetQuery). In Robert's example >> (thanks for providing that) ID2EntrezID fails to find dbGetQuery the >> second time round, but it shouldn't be relying on DBI being on the user >> search path (compare sessionInfo() after each cleanEx(), and you'll see >> that DBI is still in the list of attached packages). Fix should be >> available shortly. >> >> Robert -- please consider using R-devel during package development; >> this'll be the version in which your users will first see your package. >> >> Martin >> >>> >>> Sean >>> >>> >>> >>>> Thanks, >>>> >>>> -Robert >>>> >>>> >>>> ### Run using "R --vanilla" to be similar to R CMD check, but still >>>> fails in a normal R session as well >>>> source(file.path(R.home("share"), "R", "examples-header.R")) >>>> options(warn = 1) >>>> options(pager = "console") >>>> >>>> library('Category') >>>> >>>> assign(".oldSearch", search(), pos = 'CheckExEnv') >>>> >>>> cleanEx() >>>> >>>> nameEx("Ex1") >>>> flush(stderr()); flush(stdout()) >>>> >>>> library('org.Hs.eg.db') >>>> datPkg <- DatPkgFactory('org.Hs.eg.db') >>>> t1 <- mget('7083', ID2EntrezID(datPkg)) >>>> t1 >>>> search() >>>> >>>> cleanEx() >>>> >>>> >>>> nameEx("Ex2") >>>> flush(stderr()); flush(stdout()) >>>> >>>> library('org.Hs.eg.db') >>>> datPkg <- DatPkgFactory('org.Hs.eg.db') >>>> search() #### No DBI on the search list >>>> t1 <- unlist(mget('7083', ID2EntrezID(datPkg))) ## and this does not work >>>> t1 >>>> >>>> >>>> sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> Platform: i386-pc-mingw32/i386 (32-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 >>>> [2] LC_CTYPE=English_United States.1252 >>>> [3] LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C >>>> [5] LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] org.Hs.eg.db_2.4.6 Category_2.16.0 AnnotationDbi_1.12.0 >>>> [4] Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.28.0 DBI_0.2-5 genefilter_1.32.0 graph_1.28.0 >>>> [5] GSEABase_1.12.2 RBGL_1.26.0 RSQLite_0.9-4 splines_2.12.1 >>>> [9] survival_2.36-1 tools_2.12.1 XML_3.2-0.2 xtable_1.5-6 >>>> >>>> Robert M. Flight, Ph.D. >>>> University of Louisville Bioinformatics Laboratory >>>> University of Louisville >>>> Louisville, KY >>>> >>>> PH 502-852-1809 (HSC) >>>> PH 502-852-0467 (Belknap) >>>> EM robert.flight at louisville.edu >>>> EM rflight79 at gmail.com >>>> >>>> Williams and Holland's Law: >>>> If enough data is collected, anything may be proven by >>>> statistical methods. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. 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