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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"FailedPackage","IfPackage","File","Function","Srcref"
"biovizBase","biovizBase","biovizBase.Rcheck/biovizBase-Ex.Rout","","biovizBase/R/crunch-method.R#295
"
"branchpointer","branchpointer","branchpointer.Rcheck/branchpointer-Ex.Rout","branchpointer::makeRegions","branchpointer/R/makeRegions.R#41
"
"Cardinal","Cardinal","Cardinal.Rcheck/Cardinal-Ex.Rout","Cardinal::spatial.neighbors","Cardinal/R/spatial.R#57
"
"debrowser","debrowser","debrowser.Rcheck/debrowser-Ex.Rout","","debrowser/R/heatmap.R#38
"
"DMRcate","DMRcate","DMRcate.Rcheck/DMRcate-Ex.Rout","DMRcate::DMR.plot","DMRcate/R/DMR.plot.R#13
"
"exomePeak","exomePeak","exomePeak.Rcheck/exomePeak-Ex.Rout","","exomePeak/R/RMT.R#119
"
"fabia","fabia","fabia.Rcheck/fabia-Ex.Rout","fabia::plotBicluster","fabia/R/fabia.R#1504
"
"GenomeInfoDb","GenomicFeatures","GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.Rout","S4
Method seqlevels<-:GenomeInfoDb defined in namespace GenomicFeatures with
signature TxDb has this body.","GenomicFeatures/R/TxDb-class.R#377 "
"Glimma","Glimma","Glimma.Rcheck/Glimma-Ex.Rout","","Glimma/R/hexcol.R#32 "
"GOexpress","VennDiagram","GOexpress.Rcheck/GOexpress-Ex.Rout","VennDiagram::adjust.venn","VennDiagram/R/adjust.venn.R#42
"
"GUIDEseq","GUIDEseq","GUIDEseq.Rcheck/GUIDEseq-Ex.Rout","GUIDEseq::offTargetAnalysisOfPeakRegions","GUIDEseq/R/offTargetAnalysisOfPeakRegions.R#95
"
"hapFabia","hapFabia","hapFabia.Rcheck/hapFabia-Ex.Rout","S4 Method [<-:base
defined in namespace hapFabia with signature
IBDsegmentList#numeric#missing#IBDsegmentList has this
body.","hapFabia/R/methods-IBDsegmentList-class.R#110 "
"MassArray","MassArray","MassArray.Rcheck/MassArray-Ex.Rout","MassArray::convControl","MassArray/R/convControl.R#26
"
"methylPipe","methylPipe","methylPipe.Rcheck/methylPipe-Ex.Rout","","methylPipe/R/Allfunctions.R#635
"
"NOISeq","NOISeq","NOISeq.Rcheck/NOISeq-Ex.Rout","NOISeq::biodetection.plot","NOISeq/R/biodetection.plot.R#157
"
"pathview","pathview","pathview.Rcheck/pathview-Ex.Rout","pathview::geneannot.map","pathview/R/geneannot.map.R#31
"
"phyloseq","phyloseq","phyloseq.Rcheck/phyloseq-Ex.Rout","S4 Method mt:phyloseq
defined in namespace phyloseq with signature phyloseq#ANY has this
body.","phyloseq/R/multtest-wrapper.R#101 "
"rHVDM","rHVDM","rHVDM.Rcheck/rHVDM-Ex.Rout","rHVDM::.computeinderrtable","rHVDM/R/measurementerrorHVDM.R#23
"
"SEPA","SEPA","SEPA.Rcheck/SEPA-Ex.Rout","","SEPA/R/truetimevisualize.R#28 "
"SPLINTER","SPLINTER","SPLINTER.Rcheck/SPLINTER-Ex.Rout","","SPLINTER/R/main_splinter.R#817
"
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