On 03/31/2017 08:21 AM, Kevin RUE wrote:
Hi Martin,
Thanks a lot for systematically identifying the issue.
Looking at the issue for GOexpress now, I realise that the issue is not
in GOexpress itself, but actually within the VennDiagram package that
GOexpress imports. You actually captured that in your report:
"GOexpress","_VennDiagram_","GOexpress.Rcheck/GOexpress-Ex.Rout","VennDiagram::adjust.venn","VennDiagram/R/adjust.venn.R#42
"
In your report, GOexpress is the only Bioconductor in this situation.
I can (and will) attempt to contact the maintainer of VennDiagram, but
it just makes me wonder if you have another suggestion to deal with this
kind of issue (/i.e./, imported packages not conforming to BioC
guidelines). Is this going to raise Warnings or Errors in BiocCheck ? If
so, should we ignore such packages altogether, as long as those packages
raise check issues?
Actually, the report was generated by an R-core member, Tomas Kalibera
and the more extensive version includes all CRAN and Bioc packages. It
reflects a general effort to address these and then make them errors,
rather than warnings -- R CMD check would then fail.
Package dependencies are interesting. They are obviously hugely
important to reduce redundant code, and to fix bugs once in a single
place. But they also carry with them an additional maintenance cost. If
VennDiagram is central to your package, especially if it implements
complicated functionality, then definitely the balance is in favor of
depending on it, and working with the maintainer to address problems
that you discover.
The Bioc requirements are really about your package, especially
enforcing adequate documentation.
Martin
As a side note, I have actually already been going through GOexpress to
prepare a new major version of GOexpress (2.x.x) that will introduce S4
where relevant, and break down large functions into more sensibly-sized
steps. However, most likely that won't be ready for the next BioC release.
Best,
Kevin
On Wed, Mar 29, 2017 at 10:44 PM, Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
wrote:
On 03/29/2017 05:37 PM, Martin Morgan wrote:
Bioc developers,
R emits a warning when a condition test has length > 1
$ R --vanilla
if (letters == "a") TRUE
[1] TRUE
Warning message:
In if (letters == "a") TRUE :
the condition has length > 1 and only the first element will
be used
These are almost always programming errors.
R-3-4-branch and R-devel can be configured to report such errors, as
described on the help page for, e.g., `?"if"`
$ _R_CHECK_LENGTH_1_CONDITION_=TRUE R --vanilla
if (letters=="a") TRUE
Error in if (letters == "a") TRUE : the condition has length > 1
The attached file (thanks to Tomas Kalibera) summarizes Bioconductor
code that triggers this type of error.
Second try on the attachment
r = read.csv("long-conditional-bioc.txt")
If you maintain one of these packages (appearing in either column),
please address the error. And of course as a developer, please avoid
making the error in the future!
r = read.csv("long-conditional-bioc.csv")
r[, c("FailedPackage", "Srcref")]
FailedPackage Srcref
1 biovizBase biovizBase/R/crunch-method.R#295
2 branchpointer branchpointer/R/makeRegions.R#41
3 Cardinal Cardinal/R/spatial.R#57
4 debrowser debrowser/R/heatmap.R#38
5 DMRcate DMRcate/R/DMR.plot.R#13
6 exomePeak exomePeak/R/RMT.R#119
7 fabia fabia/R/fabia.R#1504
8 GenomeInfoDb GenomicFeatures/R/TxDb-class.R#377
9 Glimma Glimma/R/hexcol.R#32
10 GOexpress VennDiagram/R/adjust.venn.R#42
11 GUIDEseq GUIDEseq/R/offTargetAnalysisOfPeakRegions.R#95
12 hapFabia hapFabia/R/methods-IBDsegmentList-class.R#110
13 MassArray MassArray/R/convControl.R#26
14 methylPipe methylPipe/R/Allfunctions.R#635
15 NOISeq NOISeq/R/biodetection.plot.R#157
16 pathview pathview/R/geneannot.map.R#31
17 phyloseq phyloseq/R/multtest-wrapper.R#101
18 rHVDM rHVDM/R/measurementerrorHVDM.R#23
19 SEPA SEPA/R/truetimevisualize.R#28
20 SPLINTER SPLINTER/R/main_splinter.R#817
As an example the GenomeInfoDb package (row 8) has this complete
record
FailedPackage "GenomeInfoDb"
IfPackage "GenomicFeatures"
File "GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.Rout"
Function "S4 Method seqlevels<-:GenomeInfoDb defined in
namespace
GenomicFeatures with signature TxDb has this body."
Srcref "GenomicFeatures/R/TxDb-class.R#377 "
The problem was from
GenomicFeatures/R/TxDb-class.R#377
which has
mode <- GenomeInfoDb:::getSeqlevelsReplacementMode(value,
x_seqlevels0)
if (mode == -2L) {
I looked at
GenomeInfoDb:::getSeqlevelsReplacementMode
function (new_seqlevels, old_seqlevels)
{
...
and saw that its code returns a vector with length > 1 intentionally
under some specific circumstances. Also, all other uses of the
return
value of this function (in the GenomeInfoDb and GenomicFeatures
package)
test for identity of the return value via `identical()`, which
is always
a scalar. This suggests the fix
GenomicFeatures$ svn diff R/TxDb-class.R
Index: R/TxDb-class.R
===================================================================
--- R/TxDb-class.R (revision 127829)
+++ R/TxDb-class.R (working copy)
@@ -374,7 +374,7 @@
## detect the situation where the user intention is to
subset the
"real"
## seqlevels.
mode <- GenomeInfoDb:::getSeqlevelsReplacementMode(value,
x_seqlevels0)
- if (mode == -2L) {
+ if (identical(mode, -2L)) {
## "subsetting of the real seqlevels" mode
x$user_seqlevels <- value
x$user2seqlevels0 <- match(value, x_seqlevels0)
I did do some more digging around.
From the report, the failure was detected while running the
example page
script generated while checking GenomeInfoDb.
GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.Rout
So I generated this
R CMD build --no-build-vignettes GenomeInfoDb
R CMD check GenomeInfoDb_1.27.11.tar.gz
and processed it to find the error
_R_CHECK_LENGTH_1_CONDITION_=TRUE R -f
GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.R
It failed while running the example on the help page with name
"seqlevels-wrapper"
### Name: seqlevels-wrappers
### Title: Convenience wrappers to the seqlevels() getter
and setter
### Aliases: seqlevels-wrappers keepSeqlevels dropSeqlevels
renameSeqlevels
### restoreSeqlevels standardChromosomes
keepStandardChromosomes
### Keywords: methods utilities
### ** Examples
...
renameSeqlevels(txdb, sub("chr", "CH", seqlevels(txdb)))
Error in if (mode == -2L) { : the condition has length > 1
Calls: renameSeqlevels -> seqlevels<- -> seqlevels<-
Execution halted
I then could get a relatively simple reproducible example in R with
$ _R_CHECK_LENGTH_1_CONDITION_=TRUE R --vanilla
suppressPackageStartupMessages(library(GenomeInfoDb))
example("seqlevels-wrappers")
After installing the updated GenomicFeatures package, the error
did not
occur. Likewise, running GenomeInfoDb-Ex.R did not generate any
errors.
Martin
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