similar to: release build of ChemmineR failing

Hi, The R-based version of R CMD build doesn't work for me on Windows: E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase * checking for file 'meat\Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes Warning in shell(sprintf("%s > %s

A package uses VignetteEngine: knitr; the package itself does not Suggests: knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R CMD check fails indicating that a package required for checking is not declared. Is it really the intention that the original package duplicate Suggests: knitr? This is only with a recent R. In detail, with $ Rdev --version|head -3 R Under

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:

Dear R-devs, Scenario: When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces). Example: ``` R CMD check glmSparseNet_0.99.13.tar.gz * using log directory '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck' * using R Under development (unstable) (2018-06-06

Hi, Since C++ code compiled with g++ 4.6.3 on Windows (the version included in latest Rtools) now can produce things like '1.#IND' when writing doubles to a file (using the << operator), I wonder whether scan() shouldn't support those things. Right now (with recent R devel and latest Rtools) we get errors like: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,

On 05/14/2015 04:33 PM, Henrik Bengtsson wrote: > On May 14, 2015 15:04, "January Weiner" <january.weiner at gmail.com> wrote: >> >> Dear all, >> >> I am writing a vignette that requires a file which I am not allowed to >> distribute, but which the user can easily download manually. Moreover, it >> is not possible to download this file

The Bioconductor build for a package DirichletMultinomial on R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered Consequences" at http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html shows * creating vignettes ... ERROR ... Error: processing vignette ?DirichletMultinomial.Rnw? failed with diagnostics: chunk 21 (label

On 18/09/2018 2:16 PM, Marcel Ramos wrote: > Dear R-devs, > > > Scenario: > > When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces). > > Example: > > ``` > R CMD check glmSparseNet_0.99.13.tar.gz > * using log directory

As a user, I am always annoyed beyond measure that Sweave vignettes precede the code by a command line prompt. It makes running examples by simple copying of the commands from the vignette to the console a pain. I know the idea is that it is clear what is the command, and what is the output, but I'd rather precede the output with some kind of marking. Is there any other solution possible /

Dear all, I am writing a vignette that requires a file which I am not allowed to distribute, but which the user can easily download manually. Moreover, it is not possible to download this file automatically from R: downloading requires a (free) registration that seems to work only through a browser. (I'm talking here about the MSigDB from the Broad Institute,

Hi, Warnings issued at installation time are not reported by 'R CMD check'. Some of them are really important and telling something very useful to the developer. See for example this warning: http://bioconductor.org/checkResults/2.9/bioc-LATEST/globaltest/wilson2-checksrc.html Actually, there is no formal warning reported by 'R CMD check' for this package but if you scroll

On Wed, Aug 13, 2008 at 6:56 AM, Laurent Gautier <lgautier@gmail.com> wrote: > There is a chance that further changes in the handling of plotting > devices event appear; > I think that there is an ongoing effort to bring new features for R-2.8. > > What about bumping that to r-devel ? (Sorry if you already did and I missed > it). > The solution you came up with could be

I wrote some code which reads a gzipped text file directly from the web with gzcon(url()) and it works perfectly on OSX, but I cannot get it to work on linux at all, trying several different R versions and linux distributions. Any ideas? Here's an example of my code: z <- gzcon(url("ftp://ftp-private.ncbi.nlm.nih.gov/pubchem/.fetch/8897497837079742771.sdf.gz")) sdf <-

Hi, A quick and dirty (aka Rapid Application Developement) AGI script implement using bash shell. No need to invoke a 10MB perl engine to process simple asterisk agi scripts. I found it to be very useful in learning the AGI interface. For example, I learn that AGI won't execute the next command until you read the results from STDIN. Enjoy, Sunny Woo Solution Consultant Avantnix

http://www.srh.noaa.gov/fwd/productviewnation.php?pil=OKXZFPOKX&version= 0 can anyone suggest how I could set up asterisk@home to read out allowed the following text when I dial extension 850? 815 PM EST WED FEB 16 2005 .OVERNIGHT...MOSTLY CLEAR. LOWS 30 TO 35. NORTHWEST WINDS 15 TO 20 MPH WITH GUSTS UP TO 30 MPH...DIMINISHING TO 10 TO 15 MPH LATE. .THURSDAY...PARTLY CLOUDY. COOLER

Hi list, Here is an example: ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library? ??? * installing *source* package ?CoreGx? ... ??? ** using staged installation ??? ** R ??? ** data ??? *** moving datasets to lazyload DB ??? ** inst ??? ** byte-compile and prepare package for lazy loading ??? Error : in method for

Dear all, When running R CMD check on Windows XP to test my package I get the following warning message: "* checking line endings in C/C++/Fortran sources/headers ... WARNING Found the following sources/headers with CR or CRLF line endings: src/xpsDict.h" The problem is that this file is created by the compiler AUTOMATICALLY during the compilation process, and since the file is

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, since Bioconductor devel branch 3.11 started, which is operating with R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan), my package CFAssay 1.21.0 is not built on none of all three Systems, Linux, Windos and Mac. The error message refers to xy.coords which is called by R function plot.default. I found out that it has to do with the S3 object system. In my package I

>>>>> Herv? Pag?s >>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes: > Hi list, > Here is an example: > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx > ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?