similar to: R-based version of R CMD build broken on Windows

Displaying 20 results from an estimated 500 matches similar to: "R-based version of R CMD build broken on Windows"

2005 Sep 08
1
Install packages to non-default lib on Windows
We are trying to setup a Windows server that will allow any of our users to build a binary R package given a source package. The idea is to have a central R installation and allow users to install packages to their own package library for the purposes of binary package building. It seems, however, that write access to $R_HOME is required as part of the install step even when -l is used to
2018 Feb 07
1
release build of ChemmineR failing
The release version of ChemmineR is failing on windows. It seems to be a build script issue though, possibly something on your side. The package was building fine a few weeks ago and I have not modified it. Can you please have a look? Thanks. "C:/Users/BIOCBU?1/BBS-3?1.6-B/R/bin/Rscript" -e "library(rmarkdown); library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
2011 Jun 27
1
R CMD check --force-multiarch does not install all the archs for testing
Hi, Why isn't 'R CMD check --force-multiarch' installing the package for all the architectures that are going to be checked? For some packages, it only installs for the default arch ('i386'). Then testing the package for 'x64' fails. For example, Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz: ----------------------------------------------------------- *
2010 Sep 12
2
More strange R CMD build/check errors on Windows
Hi, This is a follow up to: https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html The Bioconductor daily builds have been reporting a lot of strange things lately on Windows using R-2.12. This started 2 or 3 months ago and things are not getting better with recent R-2.12. Here is a sample from today's build results. We use Windows Server 2003 R2 for the 32-bit builds, Windows
2010 Oct 11
1
'R CMD build' not cleaning the src/ folder on Windows
Hi, 'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder on Windows: D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src BUS.cpp BUS.h D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS * checking for file 'meat\BUS/DESCRIPTION' ... OK * preparing 'BUS': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package
2010 Nov 12
1
installing dependencies: binary vs source
Hi, Installing from binaries on Windows: > install.packages("multtest") Warning: dependency 'Biobase' is not available trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip' Content type 'application/zip' length 1645590 bytes (1.6 Mb) opened URL downloaded 1.6 Mb package 'multtest' successfully unpacked
2011 Mar 22
2
R_HOME path getting munged in inst/doc/Makefile on Windows
Hello, I have come across two separate packages that have a Makefile in inst/doc which use the R_HOME variable. In both cases, the path to R_HOME gets munged in such a way that commands that include R_HOME fail on Windows: For example, one Makefile, for the xmapcore package ( https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore/username/password: readonly) has this:
2013 Apr 12
2
"Failed to locate the 'texi2pdf' output file"
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
2007 Feb 05
1
Build error with last R-devel tarball
Hi, On Windows, with last R-devel tarball (r40647) from ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2007-02-04.tar.gz I get the following build error: E:\biocbld\bbs-2.0-bioc\R\src\gnuwin32> make ... ... ---------- Making package utils ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files Error in namespaceExport(ns, exports) :
2009 Apr 24
1
Managing DLLs with the same names in an R session
I am having a problem using two DLLs with the same name, but obviously located in different directories, in an R session. The troublesome package is the (Bioconductor) Rgraphviz package. It relies on (3rd party software) graphviz and imports functions from (Bioconductor) package graph. Unfortunately, the current stable release of graphviz for Windows
2013 Mar 13
1
Failed to locate 'weave' output file / vignette product does not have a known filename extension
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
2013 Oct 08
1
"Failed to locate the 'texi2pdf' output file"
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
2010 Sep 16
1
Lack of consistent cross-platform behaviour of tools:::buildVignettes()
Hi, On both Unix and Windows there is a mechanism to add variables to the environment when R is started. I noticed that, on Unix, this mechanism is not used when R is started normally at the command line but only when it's started using the 'R CMD' syntax. One problem with this is some lack of consistent cross-platform behaviour. For example: On Linux: $ echo $TEXINPUTS $
2010 Nov 10
1
installed.packages Error: subscript out of bounds
Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:
2015 Jun 24
0
system2() shortens R.home() to 8.3 form on windows
Hi, So in an interactive R session, R.home() returns the following: > R.home() [1] "D:/biocbld/bbs-3.2-bioc/R" However, if I call it from system2(), I get different results: > system2("R", "-q -e R.home()") > R.home() [1] "D:/biocbld/BBS-3~1.2-B/R" Similarly: > system2("R", "-q -e Sys.getenv('R_HOME')") >
2008 Apr 09
1
Windows problem related to using shortPathName for Sweave style file
In the process of updating R to R 2.7 alpha or R 2.7 beta for the BioConductor 2.2 builds on Windows, I have hit a snag because the BioC build system has long path names (e.g. D:\biocbld\bbs-2.2-bioc\R) and these path names are not resolving properly by MiKTeX 2.7 during vignette construction. Take, for example, the attached vignette from Biobase, Bioconductor.Rnw. I have built R from source
2008 Aug 13
0
[Bioc-devel] EBImage: Devel version on Windows not building
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
2009 Feb 07
3
New package test results available
We've added a column at http://cran.r-project.org/web/checks/check_summary.html of test results using the Sun Studio compiler: it is intended that these will be updated weekly. The Sun Studio compiler is that used on Solaris: these runs were on the Linux version. All the other platforms are using gcc 4, so this provides an opportunity for checking for use of gcc-specific features and
2007 Sep 13
1
trouble with installing Biobase package
Hi Everybody, I am having a problem with loading Biobase package. I typed 2 lines below at R prompt > source ("http://boconductor.org/biocLite.R") > biocLite (lib="/usr/local/lib/R/library") which attempted to install a bunch of packages with varying degree of success. Out of 29, 13 failed. Biobase is one of them. As a matter of fact, when I looked at logs, most
2008 Sep 05
1
Problem installing Biobase on Solaris
Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error