[BioC] Category R CMD check and not reloading required packages
Martin Morgan
mtmorgan at fhcrc.org
Thu Mar 3 15:59:22 CET 2011
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.
>>>>
>>>> _______________________________________________
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>>>>
>>>
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>>
>>
>> --
>> Computational Biology
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>> Location: M1-B861
>> Telephone: 206 667-2793
>>
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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