Re: [Bioc-devel] Package Without a Vignette

- Original Message - > From: "Zhilong Jia" > To: "Dan Tenenbaum" > Cc: "Stefan Haunsberger" , "bioc-devel" > > Sent: Saturday, April 2, 2016 11:51:24 PM > Subject: Re: [Bioc-devel] Package Without a Vignette > Hi Dan, > > *R CMD build cogena (first try):* > > * checking for file ‘c

Re: [Bioc-devel] Package Without a Vignette

Hi Dan, *R CMD build cogena (first try):* * checking for file ‘cogena/DESCRIPTION’ ... OK * preparing ‘cogena’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR Warning in engine$weave(file, quiet = quiet, encoding = enc) :

Re: [Bioc-devel] Package Without a Vignette

The nightly builds run every night (except Friday night) and if your commits are done before 5:20 PM (Seattle time) they will be reflected in the next day's build report. But you don't need the build system or even travis to see if your vignette will be built by R CMD build. All you have to do

Re: [Bioc-devel] Package Without a Vignette

Hi Dan, Thank you. I updated it. At the beginning, knitr was used but would result in errors in travis-ci, like https://github.com/ropensci/rentrez/issues/71 and https://github.com/ropensci/rentrez/commit/8ee84ba29472f56f3f92bf65511e1a29121882d4 so I changed knitr into rmarkdown and it works in

Re: [Bioc-devel] Package Without a Vignette

In DESCRIPTION change VignetteBuilder: rmarkdown to VignetteBuilder: knitr Dan - Original Message - > From: "Zhilong Jia" > To: "Stefan Haunsberger" > Cc: "bioc-devel" > Sent: Saturday, April 2, 2016 5:48:59 PM > Subject: Re: [Bioc-devel] Package Without a Vignette > Hi, > > I

Re: [Bioc-devel] Package Without a Vignette

Hi, I just found no vignette for my updated package cogena (1.5.2), though there are vignettes in the code. And the check CMD is /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cogena_1.5.2.tar.gz in http://bioco

Re: [Bioc-devel] namespace question

BTW, looks like the change has been made to R-devel: CHANGES IN R-devel NEW FEATURES * The ‘import()’ namespace directive now accepts an argument ‘except’ which names symbols to exclude from the imports. The ‘except’ expression should evaluate to a character vector (after substituting s

Re: [Bioc-devel] SVN credentials

The error with pd.genomewidesnp.6 is related to a move to a new windows toolchain (which has been discussed on this list) and the fallout affecting a package (affxparser) which pd.genomewidesnp.6 depends on. THe biovizBase issue will be resolved in the next build report (on Sunday afternoon Sea

Re: [Bioc-devel] ggbio error

Yes, the ggbio issue is fixed and this will be reflected in tomorrow's build report. Dan - Original Message - > From: "Michael Lawrence" > To: "Ludwig Geistlinger" > Cc: "bioc-devel" > Sent: Saturday, April 2, 2016 4:00:20 AM > Subject: Re: [Bioc-devel] ggbio error > I think I fixed

Re: [Bioc-devel] SVN credentials

Yes, that would be great. I will be the one making the updates. Thank you. -Krithika On Apr 2, 2016 10:45 AM, "Martin Morgan" wrote: > > > > On 04/02/2016 08:01 AM, Krithika Bhuvaneshwar wrote: >> >> Hello >> We are authors of the newly accepted CINdex package. >> >> We have not received our SVN

Re: [Bioc-devel] SVN credentials

On 04/02/2016 08:01 AM, Krithika Bhuvaneshwar wrote: Hello We are authors of the newly accepted CINdex package. We have not received our SVN credentials yet. I believe today is the last day to make changes to the package before the new release . Credentials were sent to the maintainer ('cre

[Bioc-devel] SVN credentials

Hello We are authors of the newly accepted CINdex package. We have not received our SVN credentials yet. I believe today is the last day to make changes to the package before the new release . Also our package build was error free two days ago. Yesterday there was a build error only in windows s

Re: [Bioc-devel] namespace question

Also, just btw, there are two other places where arbitrary R code can be evaluated in the NAMESPACE, but no one has abused them yet. as far as I know. The first argument to if() and the .fixes argument to useDynLib(). The latter sets the precedent for the except= behavior. Although someone forgot t

Re: [Bioc-devel] ggbio error

I think I fixed those things since the build report was generated. Michael On Sat, Apr 2, 2016 at 1:48 AM, Ludwig Geistlinger wrote: > Hi, > > I am wondering whether this is only something temporary, but given that > the new Bioc release is upcoming and packages should pass R CMD > build/check b

Re: [Bioc-devel] ggbio error

Hi, ggbio's error also cause some of my packages to fail the latest build. But I'm confident it'll get fixed before the release. Best, Leo On Sat, Apr 2, 2016 at 4:48 AM, Ludwig Geistlinger wrote: > Hi, > > I am wondering whether this is only something temporary, but given that > the new Bioc r

[Bioc-devel] ggbio error

Hi, I am wondering whether this is only something temporary, but given that the new Bioc release is upcoming and packages should pass R CMD build/check by now, I am reporting that a ggbio R CMD check error http://bioconductor.org/checkResults/devel/bioc-LATEST/ggbio/zin2-checksrc.html causes Rep