Re: [Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

Yes, please follow Hervé's instructions. On Fri, Nov 2, 2018 at 3:41 PM Håkon Tjeldnes wrote: > Just a quick question, in 3.8 we used biogenerics::lengths for ORFik, > since it was much faster than base, for our dataset 1 second vs 30 minutes. > We should change to S4 version of lengths now ? >

[Bioc-devel] Bioconductor 3.9 builds and R 3.6

Developers, We are experiencing much longer runtimes for the Bioconductor 3.9 (devel) builds which are running R 3.6. We are looking into a possible regression in R 3.6 or other causes. Because of the long run times, the sub-builds are overlapping which can saturate the machines and further ma

[Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

Hi developers, Starting with R 3.6, base::lengths() can now be treated as an S4 generic function (like base::length() or base::names()) so there is no need for us to define our own lengths() generic function in BiocGenerics. Therefore we've removed the lengths() generic from BiocGenerics (in v

[Bioc-devel] Request upstream pull --force of sanitized master branch

Dear Bioconductor, I believe I have removed all duplicate commits from the bumphunter package. The main branch in rafalab/bumphunter incorporates the new commit history. It passes 'library(devtools); build("."); install(); check("."); BiocCheck(".")' I am contacting you in accordance with it

[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

Hi, I was about to send the email below, but eventually I got it to work. I'm sharing it anyway since others might run into similar issues. Basically, I needed the latest macOS command line tools installed, but getting them installed was tricky. I installed Xcode 10.1 (10B61) from the Mac App Sto

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Thank you all very much. Jianhong. On 11/2/18, 3:03 PM, "Obenchain, Valerie" wrote: Hi Jianhong, Ghostscript is already installed on the builders. On the Nov 1 build report for Bioc 3.9, motifStack is clean on tokay2 (Windows) but failed on malbec2 (Linux). There we

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Hi Jianhong, Ghostscript is already installed on the builders. On the Nov 1 build report for Bioc 3.9, motifStack is clean on tokay2 (Windows) but failed on malbec2 (Linux). There were other packages that depended on grImports with similar errors on Linux - dagLogo and motifbreakR. I went on

Re: [Bioc-devel] GenomicFeatures

FYI I've temporarily disabled the makeTxDbFromBiomart() examples in GenomicFeatures that have been responsible for this 'R CMD check' TIMEOUT for 2-3 days in a row: https://bioconductor.org/checkResults/3.8/bioc-LATEST/GenomicFeatures/malbec1-checksrc.html Hopefully GenomicFeatures will pass CH

Re: [Bioc-devel] query regarding bfg on bioconductor repository

Just another addition. Once “master” and “RELEASE_3_8” were fixed, I made sure they work by R build and R check, and R INSTALL them. (I’m showing on the builds here) /tmp ❯❯❯ R CMD build restful_fixed * checking fo

Re: [Bioc-devel] query regarding bfg on bioconductor repository

Hello, Shweta, I have now fixed your package in “master” and “RELEASE_3_8” branches. You should sync your package on GitHub either by taking a fresh clone from git.bioconductor.org (http://bioconductor.org/developers/how-to/git/maintain-github-bioc/) or syncing it (http://bioconductor.org/dev

Re: [Bioc-devel] GenomicFeatures

Historically we used to flush the repos before a release. At some point we stopped and I could not remember why. The situation you describe below is probably it. When preparing for 3.8, we ran into the case where we had quite a few stale packages in the repos. Their 'staleness' was due to being

Re: [Bioc-devel] GenomicFeatures

Lates BiocManager It is not flagging GenomicFeatures as out of date, presumably because it doesn't exists in the repos. So in some sense it is all internally consistent. I was just surprised to not see it flagged as being out of date. I guess I am also confused about what happens at release. Is

[Bioc-devel] choosing R version dependency for existing packages

A user of MotifDb requests - sensibly, I think - that I loosen the requirement Depends: R (>= 3.5.1) which I added before the release. This seems sensible and supported by, for example, R (>= 2.10) in GenomicRanges. Is this, then, the heuristic? - new packages should depend on the lastes

Re: [Bioc-devel] GenomicFeatures

For which BiocManager::version() is this? BiocManager::valid() checks within versions, and if there's no GenomicFeatures to reference, then there is no way to flag it as out-of-date, sort of like a package you'd installed that was in neither CRAN nor Bioconductor. Though of course we'd like Gen

Re: [Bioc-devel] GenomicFeatures

Thanks Kasper. I'm looking into the error in GenomicFeatures. Martin or Marcel may have more to add but I think BiocManager::install() can only report what versions are in the repo. GenomicFeatures 1.34.0 has not built so doesn't yet exist in the repo. We archive all versions in release but not

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

My package motifStack import grImport which is depend on ghostscript. Jianhong. From: Kasper Daniel Hansen Date: Friday, November 2, 2018 at 8:55 AM To: "Jianhong Ou, Ph.D." Cc: bioc-devel Subject: Re: [Bioc-devel] Ask help to install gs tokay2 build/check Perhaps explain why On Fri, Nov 2,

[Bioc-devel] GenomicFeatures

Seem broken in release. And btw., because it is broken, when I run BiocManager::valid() it doesn't report GenomicFeatures as out of date, despite the fact that I have version 1.33.2 installed, and there are newer versions in the 1.33.x hierarchy and the "right" (but broken) version in Bioc 3.8 i

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Perhaps explain why On Fri, Nov 2, 2018 at 8:19 AM Jianhong Ou, Ph.D. wrote: > Hi, > > Is it possible to install ghostscript in tokay2 for development package > build? > > Yours Sincerely, > > Jianhong Ou > > Email: jianhong...@duke.edu > Bioinformatician II > Depart

[Bioc-devel] Ask help to install gs tokay2 build/check

Hi, Is it possible to install ghostscript in tokay2 for development package build? Yours Sincerely, Jianhong Ou Email: jianhong...@duke.edu Bioinformatician II Department of Cell Biology Duke University School of Medicine Durham, NC, 27710 Confidentiality Notice: T