similar to: Install packages to non-default lib on Windows

Displaying 20 results from an estimated 2000 matches similar to: "Install packages to non-default lib on Windows"

2010 Jun 10
1
R-based version of R CMD build broken on Windows
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
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
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
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
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:
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) :
2004 Oct 05
1
How to install affy package in R?
Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] "ProgressBarText" [1]
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:
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 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 Nov 15
1
unable to view vignette in R
Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:
2010 Jul 08
2
package installation for Windows 7
Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =
2006 Jul 19
1
[BioC] Errors using biocLite on Apple OS X
The warnings from make.packages.html() on the Apple Mac OS X platform can be dealt with as follows: ------------------------------------------------ (1) make.packages.html() uses the function tempdir() and attempts to create a temporary directory in the default location /tmp/ which fails due to the /tmp directory architecture on the Mac. I set up a .Renviron file in my user account
2003 Sep 11
1
potentially nasty interaction between R 1.8.0 and tetex
I've been having problems building vignettes in bioconductor packages with R-devel. Turns out that Rdevel/share/texmf/hyperref.cfg wants Blue and Red predefined, when only blue and red are defined (as of rsync Rdevel, Sept 10th). This is on a Debian unstable system (Sept 9th version). Might not apply to all other tetex systems. Seems to have bitten the bioconductor build system, though.
2003 Sep 05
2
S4 Method Collisions with "[" (PR#4075)
Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >
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
2012 Nov 26
1
A problem subsetting a data frame
Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in
2006 Oct 11
1
Possible bug in accessing methods documentation?
Hi, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")