[Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

Hi bioconductor devs, The BSgenomeViews class has been very useful in efficiently propagating metadata for running Biostring operations. I noticed something unexpected when iterating over views - it seems to return the Biostrings object instead of a single length Views object, and thus loses the

[Bioc-devel] Bioconductor 3.5 release: db0, OrgDb and TxDb packages

Hi, The new db0, OrgDb and TxDb packages are now available in the devel branch. # db0: Updated all 19: anopheles.db0_3.4.2.tar.gz chicken.db0_3.4.2.tar.gz fly.db0_3.4.2.tar.gz pig.db0_3.4.2.tar.gz xenopus.db0_3.4.2.tar.gz arabidopsis.db0_3.4.2.tar.gz chimp.db0_3.4.2.tar.gz

Re: [Rd] Very hard to reproduce bug (?) in R-devel

> > Also my suspicion, can you try without having JIT enabled? > The results for different JIT levels. I ran compiler::enableJIT() before sourcing the test file: 3: error 2: error 1: OK 0: OK -Winston [[alternative HTML version deleted]] __

Re: [Rd] Very hard to reproduce bug (?) in R-devel

> > Apologies in advance if this is just stating the obvious, but let me try > and put some general ideas on the table. These are great ideas, thanks. > - is anything non-deterministic involved? (Doesn't sound so, but...) > There was an environment where items were added, and the names of

Re: [Rd] Very hard to reproduce bug (?) in R-devel

On 05.04.2017 23:54, peter dalgaard wrote: On 05 Apr 2017, at 20:40 , Winston Chang wrote: I think there's a good chance that this is due to a bug in R. I have been trying to track down the cause of the problem but haven't been able find it. -Winston Apologies

Re: [Rd] Very hard to reproduce bug (?) in R-devel

> On 05 Apr 2017, at 20:40 , Winston Chang wrote: > > I think there's a good chance that this is due to a bug in R. I have > been trying to track down the cause of the problem but haven't been > able find it. > > -Winston Apologies in advance if this is just stating

Re: [Rd] Very hard to reproduce bug (?) in R-devel

-Wall -pedantic -O2 -mtune=native -fsanitize=address The output looks like this (it should be in order --1--, --2--, --3--, repeat): 20170405-213410.095858-18 20170405-213420.085451-17 20170405-213550.084947-16 --1-- 20170405-213410.095858-18 20170405-213420.085451-17 20170405-213550.084947-16 --1

Re: [Rd] Very hard to reproduce bug (?) in R-devel

On 5 April 2017 at 15:46, Winston Chang wrote: | On Wed, Apr 5, 2017 at 2:24 PM, Robert McGehee | wrote: | | > Winston, | > I had a similar experience to you tracking down an insanely difficult bug | > in my R code that "disappeared" whenever slight changes were

Re: [Rd] Very hard to reproduce bug (?) in R-devel

at's due to the cat() calls being executed in the wrong > order, or if it's simply being printed or buffered in the wrong order. > > This is the code in question that cat()s to stderr: > https://github.com/rstudio/pool/blob/0724ad9/R/scheduler.R#L74-L90 > while (TRUE) { > tasks <

Re: [Rd] Very hard to reproduce bug (?) in R-devel

On Wed, Apr 5, 2017 at 2:24 PM, Robert McGehee wrote: > Winston, > I had a similar experience to you tracking down an insanely difficult bug > in my R code that "disappeared" whenever slight changes were made to the > script (e.g. like adding cat() statements). In my

Re: [Rd] Very hard to reproduce bug (?) in R-devel

cat(ls(private$scheduledTasks), "--2--\n", file = s) cat(t, "--3--\n", file = s) task <- private$scheduledTasks[[t]] rm(list = t, envir = private$scheduledTasks) task() } Without going into too much detail, it should print l

Re: [Rd] Very hard to reproduce bug (?) in R-devel

cat(ls(private$scheduledTasks), "--2--\n", file = s) cat(t, "--3--\n", file = s) task <- private$scheduledTasks[[t]] rm(list = t, envir = private$scheduledTasks) task() } Without going into too much detail, it should print lines of te

[Bioc-devel] Using R Markdown for creating reproducible manuscripts – new blog post from eLife Labs

[With apologies for cross-posting] Hi all, We have today published a blog post on eLife Labs about how scientists can use the dynamic document language, R Markdown, for creating reproducible manuscripts. At eLife, we aim to make the communication of results more beneficial for the scientific

[Bioc-devel] Commiting from git to svn

Dear all, Short problem: I am a trying to sync my new package BioCor git repository with the Bioconductor svn repository. But I am failing when I do git svn dcommit. Long history of the problem I did some changes on my master branch (where I developed until now) then I used the update_remotes.sh

Re: [Bioc-devel] Check error on malbec2

Yes, it is. Aimin On Wed, Apr 5, 2017 at 7:20 AM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Are these permanent system files or files that are created during > examples/vignettes? > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of

Re: [Bioc-devel] Check error on malbec2

Are these permanent system files or files that are created during examples/vignettes? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Aimin

Re: [Rd] Bug report: POSIX regular expression doesn't match for somewhat higher values of upper bound

> > on Tue, 4 Apr 2017 08:45:30 + writes: > Dear Sirs, > while >> regexpr('(.{1,2})\\1', 'foo') > [1] 2 > attr(,"match.length") > [1] 2 > attr(,"useBytes") > [1] TRUE > yields the correct match, an

Re: [Rd] Very hard to reproduce bug (?) in R-devel

> Winston Chang > on Tue, 4 Apr 2017 15:29:40 -0500 writes: > I've done some more investigation into the problem, and it is very > difficult to pin down. What it looks like is happening is roughly like this: > - `p` is an environment and `p$e` is