similar to: Creating a reference manual during R CMD build

Hi, The following command: R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test genefu-package.Rd run against this file: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-package.Rd (username: readonly; password: readonly) produces a very verbose error (see below) with R version 2.15.0 alpha (2012-03-07 r58622). The .Rd file has these lines in it: Version: \tab

I know this has come up before on R-help (http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal-identical-which-requires-6-td4548460.html) but I have a concise reproducible case that I wanted to share. Also, please note the Bioconductor scenario which is potentially seriously impacted by this. The issue arises when a binary version of a package (like my example package below) is built

Hi, Unfortunately it looks like this problem has somehow been reintroduced. I am now trying to build R-devel 54683 from source, again following the manual. I get the same error as below: gcc -std=gnu99 -I../../include -DHAVE_CONFIG_H -O3 -Wall -pedantic -c zutil.c -o zutil. o make[4]: *** No rule to make target `Rzlib.def', needed by `Rzlib.dll'. Stop. make[3]: *** [rlibs] Error 1

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OrganismDbi [...] Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : Failed to locate the 'texi2pdf' output file (by

Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved. It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release. See the complete thread

Hello, I'm seeing three different vignette-related errors with recent versions of R-3.0.0 alpha. First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ?BitSeq.Rnw' failed with diagnostics: Failed to locate the ?weave? output file (by engine ?utils::Sweave?) for

If I f = function() {} package.skeleton("PkgA", "f", path="/tmp") and then edit man/PkgA-pacakge.Rd to read in part \description{ More about what it does (maybe more than one line) \Sexpr{1} } and then R CMD build PkgA I end up with Saving output to ?/tmp/PkgA/build/PkgA.pdf? ... Warning in file.create(to[okay]) : cannot create file

Hi, The page http://cran.r-project.org/bin/windows/base/rtest.html has a link to: http://cran.r-project.org/bin/windows/base/R-2.15.0rc-win.exe However, clicking on that link gives a 404 "Object not found' error. FYI. Dan

----- Original Message ----- > From: "Simon Urbanek" <simon.urbanek at r-project.org> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org> > Cc: "R-devel" <r-devel at r-project.org> > Sent: Monday, January 12, 2015 5:50:35 PM > Subject: Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel) > > Dan, > > On

On 12/07/2018 7:30 AM, G?bor Cs?rdi wrote: > On Thu, Jul 12, 2018 at 12:23 PM Duncan Murdoch > <murdoch.duncan at gmail.com> wrote: >> >> On 12/07/2018 6:33 AM, G?bor Cs?rdi wrote: >>> I would like to create \examples{} in the manual dynamically, and >>> while it is possible to do this with a \Sexpr at the top level, R CMD >>> check issues a

On Thu, Jul 12, 2018 at 12:23 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > > On 12/07/2018 6:33 AM, G?bor Cs?rdi wrote: > > I would like to create \examples{} in the manual dynamically, and > > while it is possible to do this with a \Sexpr at the top level, R CMD > > check issues a warning for it. (See below.) > > > > Is it intentional that

Hi, After updating R-2.12 on the Bioconductor build system about 1 week ago (we update R every 4-6 weeks for our devel builds), we've started to see something never seen before on Windows: for some BioC packages, 'R CMD build' would produce no output at all (0 byte) and, of course, no source tarball. Even though, the code returned by the command is 0! See an example of this is here:

I would like to create \examples{} in the manual dynamically, and while it is possible to do this with a \Sexpr at the top level, R CMD check issues a warning for it. (See below.) Is it intentional that \Sexpr is not allowed at the top level? The Rd grammar allows this, but R CMD check does not. Is there any other way to generate/modify the \examples{} section dynamically? Thanks, Gabor In

Hi, Kind of related to the new R-based 'R CMD build' script being sometimes confused on Windows (as reported here a couple of weeks ago https://stat.ethz.ch/pipermail/r-devel/2010-June/057759.html), I also started to observe that the new R-based 'R CMD check' script gets also confused sometimes on Windows in a random way. It seems that sometimes (maybe 1% of the times) running

Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan ---------- Forwarded message ---------- From: Stefan McKinnon H?j-Edwards <Stefan.Hoj-Edwards at agrsci.dk> Date: 2011/10/4 Subject: Re:

On Thu, Jul 12, 2018 at 2:30 PM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote: > > On Thu, Jul 12, 2018 at 2:21 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > > I think I found the bug. The tools::checkRd function only processes > > \Sexpr's with "stage=render". I think the author (who might have been > > me, I forget) assumed that

On 12/07/2018 9:46 AM, G?bor Cs?rdi wrote: > On Thu, Jul 12, 2018 at 2:30 PM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote: >> >> On Thu, Jul 12, 2018 at 2:21 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote: >>> I think I found the bug. The tools::checkRd function only processes >>> \Sexpr's with "stage=render". I think the author

Thank you Dan but it isn't my tests that are failing (all of them pass without problem) but one of the examples from the inst/examples directory. I did try, however, to start R with the environmental variables as you suggest but it had no effect on my tests. Charles On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote: > > > ----- Original Message

We were also able to reproduce the issue on Windows Server 2012. If there's anything we can do to help please let me know; Elliot Waingold (CC'd here) can provide access to the VM we used for testing if that's of any help. # David Smith -- David M Smith <davidsmi at microsoft.com> R Community Lead, Revolution Analytics (a Microsoft company)? Tel: +1 (312) 9205766 (Chicago IL,

Hi, It's unfortunate that with recent revisions of R 2.13 (this appeared in revision 54640, March 2), 'R CMD build' now removes empty dirs in the package. People might have good reasons for having empty dirs in their packages. For example, in Bioconductor, we have some tools to automatically generate annotation packages and those tools are implemented in software packages that use