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?
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> 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
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee
>> or agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited. If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
