Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

Thanks Daniel. Glad to see the end of that monkey business, my analyses were going bananas. On Fri, Apr 26, 2019 at 3:41 PM Van Twisk, Daniel < daniel.vantw...@roswellpark.org> wrote: > I've pushed new 3.8.2 orgdbs that should propagate soon. They do not have > this issue. >

[Bioc-devel] 答复: package rJava can not be loaded in build system OS X

Thank you for fast reply! Best, Zheng 发件人: Pages, Herve 发送时间: 2019年4月25日 15:44 收件人: Zheng Wei; bioc-devel 主题: Re: [Bioc-devel] package rJava can not be loaded in build system OS X The problem has been addressed. However, the fix came after the nightly

Re: [Bioc-devel] package size issue

Interesting observation Boris. The software packages currently have 1261 pdf vignettes and 983 html vignettes in BioC 3.9. Here are some quick stats that confirm Boris' observation (sizes are in bytes): > summary(pdf.sizes)     Min.  1st Qu.   Median Mean  3rd Qu. Max.     5267  

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

I've pushed new 3.8.2 orgdbs that should propagate soon. They do not have this issue. From: Bioc-devel on behalf of Pages, Herve Sent: Thursday, April 25, 2019 9:19:35 PM To: Aaron Lun; Vincent Carey Cc: Bioc-devel; jmac...@u.washington.edu Subject: Re:

[Bioc-devel] Fixes to db0s and org.db's + rebuild annotations depending on these

Hello Bioconductor Community We experienced some problems with our most recent annotations. The following updated orb.dbs and db0s should correct the issue. These is an existing problem with the UCSC's mouse knownGene resource the will be corrected on Monday next week. Please rebuild any

Re: [Bioc-devel] package size issue

I've recently been struggling with this and found to my surprise that even basically empty HTML vignettes are 1Mb in size due to the extensive Javascript they contain. PDF vignettes are much smaller. Perhaps this helps. Cheers, Boris > On 2019-04-26, at 17:44, Jianhai Zhang wrote: > >

Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9

Hi Qiang, On 4/26/19 11:47, Hu, Qiang wrote: > Hi all, > > > Could you please help to check whether the required python package "cwltool" > is installed and works in malbec2 and celaya2? > > Here is part of the error log in malbec2: > > $cwltool --version > > ... > >

Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9

Hi all, Could you please help to check whether the required python package "cwltool" is installed and works in malbec2 and celaya2? Here is part of the error log in malbec2: $cwltool --version ... pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not found and is

[Rd] Error in glm(..., family=quasi(..., variance=list(...)))

In a glm() call using a quasi() family, one may define a custom variance function in the form of a "list containing components varfun, validmu, dev.resids, initialize and name" (quoting the help page for family). In trying to do so, I run into the following issue that I have not seen discussed

Re: [Bioc-devel] R CMD check WARNING file link 'x' in package 'y' does not exist and so has been treated as a topic

Hi, I’ve actually had the exact same problem. The solution for me was to change \link[pkg:foo]{bar} where foo is the actual .Rd filename in the original package. Downloading the limma source reveals there is an Rd file named 01Introduction.Rd, without the dot as you had it. So it would look

Re: [Rd] configure script issue with -flto with recent gcc and system ar/ranlib

On 4/25/19 6:11 PM, Thomas König wrote: Hi Tomas, On 4/23/19 2:59 PM, Thomas König wrote: Hi, there can be an issue with recent gcc where the system-installed "ar" and "ranlib" commands cannot handle LTO binaries.  On compilation, this manifests itself with error messages claiming that they

[Bioc-devel] R CMD check WARNING file link 'x' in package 'y' does not exist and so has been treated as a topic

Dear all, I’ve had some trouble clearing the WARNING from R CMD check on tokay2 for my package piano (http://bioconductor.org/checkResults/3.9/bioc-LATEST/piano/tokay2-checksrc.html ). As an example, I get this warning: Rd warning in diffExp.Rd:75: “file link '01.Introduction' in package

[Bioc-devel] Important Change to Release 3.9

Hello maintainers, We have decide to delay the release 3 days to allow the build report to stabilize from some recent changes/issues that have since been remedied (connectivity issues, missing system dependencies, etc...) The release of Bioc3.9 is now schedule for Friday May 3 and the branch

[Rd] R 3.6.0 is released

The build system rolled up R-3.6.0.tar.gz (codename "Planting of a Tree") this morning. The list below details the changes in this release. You can get the source code from http://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you.

[Rd] A bug in file.copy(), deletes file contents

Hi, I've discovered a way to accidentally delete all your files with file.copy(). This involves copying a directory to itself by bypassing the check `if (recursive && to %in% from)` by pointing to a directory with two differing ways. Here I'm copying the directory foo to itself: