Re: [Bioc-devel] biocLite() repository not available for Bioconductor 3.4

2016-10-14 Thread Hervé Pagès
The software repository for bioc 'devel' is now partially back on-line. Unfortunately the Mac binaries didn't make it yet and won't before tomorrow Oct Saturday 15 around 5 pm EST. Sorry for the inconvenience, H. On 10/14/2016 08:54 AM, Martin Morgan wrote: Bioconductors! The software

Re: [Bioc-devel] Build failure for new package

2016-10-14 Thread Martin Morgan
On 10/14/2016 05:09 PM, Tyler Smith wrote: Hi, My flowPloidy package has been accepted into the devel branch, and I've now received a warning about a build failure: http://master.bioconductor.org/checkResults/3.4/bioc-LATEST/flowPloidy/malbec1-buildsrc.html The error indicates that the

Re: [Bioc-devel] Need help

2016-10-14 Thread Laurent Gatto
Dear Arvind, This question would have been more appropriate on the support site, rather than the developer mailing list. The output of sessionInfo() would have been useful too, so what comes is speculation based on the BiocUpgrade message. I assume you are using Windows, otherwise your mzR

[Bioc-devel] Need help

2016-10-14 Thread Arvind Korwar
Dear All, I am coming across following error. Warning message:In fun(libname, pkgname) : mzR has been built against a different Rcpp version (0.12.6) than is installed on your system (0.12.7). This might lead to errors when loading mzR. If you encounter such issues, please send a report,

[Bioc-devel] Build failure for new package

2016-10-14 Thread Tyler Smith
Hi, My flowPloidy package has been accepted into the devel branch, and I've now received a warning about a build failure: http://master.bioconductor.org/checkResults/3.4/bioc-LATEST/flowPloidy/malbec1-buildsrc.html The error indicates that the flowPloidy vignette failed to compile, because the

Re: [Bioc-devel] biocLite and useDevel

2016-10-14 Thread Dan Tenenbaum
Probably related to: https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009897.html Dan - Original Message - > From: "Kasper Daniel Hansen" > To: "bioc-devel" > Sent: Friday, October 14, 2016 9:07:34 AM > Subject:

[Bioc-devel] biocLite and useDevel

2016-10-14 Thread Kasper Daniel Hansen
This is unexpected, to me at least (below). I source biocLite and set useDevel(TRUE) and it does not switch to current devel branch. Perhaps this has to do with branches and stuff. Breaks current Travis setup. Perhaps this is just a hiccup which will go away. # R-3.3 R version 3.3.1 RC

[Bioc-devel] biocLite() repository not available for Bioconductor 3.4

2016-10-14 Thread Martin Morgan
Bioconductors! The software repository for bioc 'devel' is unfortunately not available for the next several hours. We'll announce here when it is back on-line. Sorry for the inconvenience Martin This email message may contain legally privileged and/or...{{dropped:2}}

Re: [Bioc-devel] maftools build error

2016-10-14 Thread Obenchain, Valerie
Hi Anand, Looks like maftools is clean on the Oct 12 report: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ We've had some hiccups ... and it looks like that problem is transient. You can safely ignore it for now. Thanks for keeping an eye on the build report. Valerie On

Re: [Bioc-devel] msPurity check failure on Windows

2016-10-14 Thread Thomas Lawson
Hi Martin/all It looks like the build/check [1] is still using an older version of the code (v0.99.9) so it is still failing the check in Windows. i.e. it has not updated to version (v0.99.12) [2] of the code. Is this going to be a problem for the package to be accepted into the next stable