[Bioc-devel] condition tests on vectors with length greater than 1

Martin Morgan martin.morgan at roswellpark.org
Wed Mar 29 23:44:32 CEST 2017


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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-------------- next part --------------
"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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