Hi Martin,
On 03/29/2017 02:37 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.
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!
I promess I won't do it again ;-)
Thanks for fixing the condition test in GenomicFeatures!
H.
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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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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