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")