Search Archives

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...

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...

Dear all, I have some simple functions to create badges for using in README or github pages. See ggtree project website <https://guangchuangyu.github.io/ggtree/> and README <https://github.com/GuangchuangYu/ggtree/blob/master/README.md> as examples. I...

Dear all, I found many peoples still using (and asking questions of) out-dated branch of Bioconductor packages that are no longer maintained.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...

Dear all, My package, ggtree, for visualizing phylogenetic tree will be released in BioC 3.1. It's not a simple tree viewer. The design of this package is to facilitate adding different types of annotation in multiple layers. Internally...

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...

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...

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 <dtenenba at fredhutch.org> wrote: > > > ----- Original Message ----- > > From: "Yu, Guangchuang" <gcyu...

I found the issue was filed by yihui half month ago on github, https://github.com/Bioconductor/BiocStyle/issues/18, and the solution is quite intuitive by removing those un-supported paramters (self_contained, lib_dir, output_dir). Hope it...

Der Vincent, RNGkind("L'Ecuyer-CMRG") works as using mc.set.seed=FALSE. When mc.cores changes, the output is not reproducible. I think this issue is also of concern within the Bioconductor community as parallel version of permutation test...

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...

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...

There is one possible solution posted in http://stackoverflow.com/questions/30610375/how-to-run-permutations-using-mclapply-in-a-reproducible-way-regardless-of-numbe/30627984#30627984 . As Kasper suggested, it's not a proper way to use set.seed...

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...

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...

Dear Dan, Thanks for the update, this is really helpful. I think many users are new to R and they just google search their issue and find out a Bioconductor package may solve their issue. The problem is the landing...