[BioC] Category R CMD check and not reloading required packages

[Robert M. Flight]

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?

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

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