Thanks a lot for your swift and helpful reply, Henrik! Yes, I could reproduce the error on my local system by adding "_R_CHECK_LENGTH_1_LOGIC2_=verbose" to my .Renviron file. I will fix the errors and push fixes soon.
Thanks again, Ulrich -----Original Message----- From: Henrik Bengtsson <henrik.bengts...@gmail.com> Sent: Donnerstag, 17. Juni 2021 17:21 To: bodenho...@bioinf.jku.at Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Build error "failure: length > 1 in coercion to logical" not reproducible On Thu, Jun 17, 2021 at 2:32 AM <bodenho...@bioinf.jku.at> wrote: > > Dear colleagues, > > It seems to me that, starting with the latest BioC devel branch > (3.14), the build systems have become more pedantic about logical > vectors of length > 1 in conditions. Two of the packages I am maintaining, > 'kebabs' and 'procoil' > currently fail to build. Surely I want to fix this. However, I cannot > reproduce these errors on my local system (R 4.1.0 alpha on Ubuntu > 18.04 LTS). The discussions > https://support.bioconductor.org/p/9137605/ and > https://github.com/Bioconductor/BBS/issues/71 have pointed me to the > setting "_R_CHECK_LENGTH_1_CONDITION_=verbose". > > First question: Can anybody confirm that this has been changed in the > recent devel? Not a Bioc maintainer, but yes, the Bioc build system added this on May 22, 2021 in order to catch similar bugs in package vignettes, cf. https://community-bioc.slack.com/archives/CLUJWDQF4/p1622062783020300?thread_ts=1622053611.008100&cid=CLUJWDQF4 > > Second question: I have tried to include > "_R_CHECK_LENGTH_1_CONDITION_=verbose" in my .Renviron file and it > seems that my R session respects that. However, when I run 'R CMD > build' on the aforementioned packages, they still build fine. The > suggestions in > https://github.com/Bioconductor/BBS/issues/71 don't work for me either > (maybe I have done something wrong). I would actually like to > reproduce the errors in my local system, since this will help me > fixing the errors and testing the changes. So can anybody give me > advice how I can make my local installation to check for logical > vectors of length > 1 in conditions more strictly? You want to set: _R_CHECK_LENGTH_1_LOGIC2_=verbose That one catches bugs where x && y or x || y is called with length(x) > 1 or length(y) > 1. Using: _R_CHECK_LENGTH_1_CONDITION_=verbose catches bugs where if (x) { ... } and similar conditions are called with length(x) > 1. In your case, a reproducible minimal example is: Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_"="verbose") files <- c("a", "b") files <- Rsubread:::.check_and_NormPath(files) ... Error in is.na(files) || is.null(files) : 'length(x) = 2 > 1' in coercion to 'logical(1)' The problem is that there's a is.na(files) || is.null(files) in the code, where > is.na(files) [1] FALSE FALSE > is.null(files) [1] FALSE so, we have an x || y case with length(x) > 1. /Henrik > > Thanks a lot in advance, > Ulrich > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
