[Bioc-devel] annotation data not updated?

Dear all, I just upgraded BioC to 3.6 and found that the data source of org.Hs.eg.db and GO.db is still half year ago. I was wondering whether these packages had been updated in current release. > org.Hs.eg.db OrgDb object: | DBSCHEMAVERSION: 2.1 | Db type: OrgDb | Supporting package: Annotation

[Bioc-devel] badges for Bioconductor package

Dear all, I have some simple functions to create badges for using in README or github pages. See ggtree project website and README as examples. I think someone may also interesting in using t

[Bioc-devel] report package issue to Bioconductor

Dear all, Some packages never updated after they publish a paper, and they just ignore bug report. I think we need somewhere, maybe on github, to post code review and Bioconductor core team can take action if maintainer fail to fix issue. Here is a quick look of the CorMut package: https://gist.

Re: [Bioc-devel] BiocStyle issue

, Leonardo Collado Torres wrote: > Guangchuang, you can see at > https://github.com/Bioconductor/BiocStyle/issues/19 (the main github > repo for this package) that this issue is already been reported and > will be addressed asap by BiocStyle's maintainer. > > On Tue, Nov

[Bioc-devel] BiocStyle issue

Dear all, I recompile my package and it throw the following error when building vignettes: unused arguments (self_contained, lib_dir, output_dir) I search ?opts_knit, and couldn't find these parameters. In ?opts_knit, I find *self.contained* instead of *self_contained*. I remove the dependenc

Re: [Bioc-devel] notify out-dated branches

inming Jiao" <20907...@zju.edu.cn> > > To: "Dan Tenenbaum" > > Cc: "Yu, Guangchuang" , "bioc-devel" < > bioc-devel@r-project.org> > > Sent: Sunday, June 12, 2016 7:33:02 PM > > Subject: Re: Re: [Bioc-devel] notify out-dated

[Bioc-devel] notify out-dated branches

Dear all, I found many peoples still using (and asking questions of) out-dated branch of Bioconductor packages that are no longer maintained. I think it would be great to have a message notifying them when they are browsing the web page of out-dated branches, just like we have a message for devel

Re: [Bioc-devel] commit fail in devel branch

Dear Dan, Thank you for your quick reply! It works by specifying my username and password. Bests, Guangchuang On Wed, Nov 4, 2015 at 9:16 AM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Yu, Guangchuang" > > To: "bioc-devel" &g

[Bioc-devel] commit fail in devel branch

Dear all, I found devel branch reject my commit by throwing the following msg: ➜ clusterProfiler git:(master) svn ci -m 'facet dotplot' svn: E175013: Commit failed (details follow): svn: E175013: Access to '/bioconductor/!svn/me' forbidden There maybe some file permission issue. Bests, Guangch

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Dear Dan, I am talking about the DOSE package, not GOSemSim. FYI, I have figured out how to commit to Bioc svn via the following command: git checkout devel rm -rf .git/rebase-apply git reset --hard 418b1dd git svn rebase git merge master --no-edit git svn dcommit --add-author-from see https://

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Dear Dan, Thanks for your information. I have successfully commit to Bioc svn via github yesterday, see https://github.com/Bioconductor-mirror/DOSE/commits/master. Today I modify some code, and push it to github. But when I try to push it to Bioc svn, it throw error indicating that everything is

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Dear Dan, I update my package GOSemSim(https://github.com/GuangchuangYu/GOSemSim), with the following steps: 1. delete the git-svn-bridge 1. bash /path/to/update_remotes.sh 2. git checkout devel 3. git checkout master 4. git merge devel All was fine without any error. But when I follow the in

Re: [Bioc-devel] reproducible with mclapply?

>> > >> > >> > >> > On Wed, Jun 3, 2015 at 5:17 PM, Vincent Carey < >> st...@channing.harvard.edu> >> > wrote: >> > >> >> Hi, this question belongs on R-help, but perhaps >> >> >> >> >>

Re: [Bioc-devel] reproducible with mclapply?

angchuang On Wed, Jun 3, 2015 at 5:17 PM, Vincent Carey wrote: > Hi, this question belongs on R-help, but perhaps > > https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/RngStream.html > > will be useful. > > Best regards > > On Wed, Jun 3, 2015 at 3:11 A

[Bioc-devel] reproducible with mclapply?

Dear all, I have an issue of setting seed value when using parallel package. > library("parallel") > library("digest") > > set.seed(0) > m <- mclapply(1:10, function(x) sample(1:10), + mc.cores=2) > digest(m, 'crc32') [1] "4827c80c" > > set.seed(0) > m <- mclapply(1:10, function(x)