[Bioc-devel] Catching SVN up to Github

Hi all, Since our package, "trena", was accepted, we've made some pretty extensive changes to the package on Github. Our version has so far jumped from 0.99.10 to 0.99.135. These changes are all contained on a forked version of the Bioconductor mirror, as specified (https://www.bioconductor.org/

[Bioc-devel] Default Coverage Value

Hello, The coverage function is still inconvenient to use with a vector of weights to convert a GRanges metadata column into a RleList object. "The coverage method for GRanges could gain a default value argument." - Michael Lawrence, January 2013. "Something like coverage(foo, bar, ...,

Re: [Rd] matrices with names

Not always, see what happens with lapply: > x<-matrix(12,1,1) > names(x)<-"one" > y<-matrix(1,1,1) > names(y)<-"one" > dput(lapply(x,`+`,e2=y)) structure(list(one = structure(13, .Dim = c(1L, 1L))), .Names = "one") >dput(lapply(x,`+`,e2=1)) structure(list(one = 13), .Names = "one") Prof. Ripley

Re: [Bioc-devel] git transition for projects with prior git history

Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to force the merge: https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories Cheers, Vlad On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew < andrew_mcda...@urmc.rochester.edu> wrote: > Is there a

[Bioc-devel] git transition for projects with prior git history

Is there a recommended recipe to utilize the git.bioconductor.org remote with an existing git repo that has non-zero history? I tried adding the git.bioconductor.org as a remote, making a branch, and then checking out a branch on that

Re: [R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file

Thanks, Duncan. The tarball was created using the standard R CMD build function. But, as far as I can tell, I must have built the tarball with a previous R version (e.g., version 3.3), which did not contain the partial.rdb file when constructing the tarball, and then checked with the dev version.

Re: [R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file

On 26/07/2017 12:23 PM, Phil Chalmers wrote: Yes, I can see the partial.rdb file in the list, also in entry 28. So I believe the problem is on the CRAN build. For the rest of the list: This claim is incorrect. The tarball that was submitted to CRAN did not contain the partial.rdb file. The

Re: [Bioc-devel] xcms adjustRtime-obiwarp Error

Dear Riccardo, I will look closer into this. In the meantime it might help if you try a different binSize in the ObiwarpParam. Also, could you please add an issue with this error on https://github.com/sneumann/xcms ? I can then track and relate all changes to the issue. thanks, jo On 27 Jul

[Bioc-devel] xcms adjustRtime-obiwarp Error

Dear xcms devel, running the latest stable xcms version I get the following error: > xod <- adjustRtime(xod, param = ObiwarpParam()) Sample number 3 used as center sample. Aligning pl55_06h_01.mzXML against pl55_03h_01.mzXML ... Error: BiocParallel errors element index: 1, 2, 3, 4, 5 first

[Bioc-devel] Vignette for xcms fails to build on tokay1

Dear all, one of the xcms vignettes fails to build on tokay1 recently with the error message: Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I

Re: [Rd] dir.create typo in manual An Introduction to R

> John Blischak > on Wed, 26 Jul 2017 16:22:22 -0500 writes: > In the section FIles and Directories in the manual An Introduction to > R it refers to the function create.dir: >