[R] Installing packages
Hello, I have a problem when making packages with version 2.6.1. I have a package which I could install in version 2.5.1. I have made some modifications of the package, and I would like to install it to 2.6.1. I check the package with R CMD check, I build it with R CMD build and when I try to install it it gives me an error, it tries to install something like R.css and tells me that cannot open the DESCRIPTION file. Then, I made the same procedure with version 2.5.1 and it worked fine. I am using Windows Vista and I changed the PATH environment variable to version 2.6.1. Any suggestion to solve the problem? Best regards, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing packages based on the license
Hello, I would like have an automatic way to avoid installing packages that I cannot use due to license restrictions. For example, the conf.design package is limited to non-commercial use, and since I work for a for-profit business, I cannot use it. I found out about the license terms of conf.design by chance; I would like to avoid any possibility of a mistake in the future. Is there some clever combination of grep and install.packages that I could use to limit my downloads to, say, GPL-only packages? Thanks, Ted Ted Mendum | Senior Scientist Warner Babcock Institute for Green Chemistry 66 Cummings Park, Woburn, MA 01801 p: 781-937-9000 f:781-937-9001 [EMAIL PROTECTED] www.warnerbabcock.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing packages based on the license
On Wed, 26 Nov 2008, Ted Mendum wrote:
Hello,
I would like have an automatic way to avoid installing packages that I cannot
use due to license restrictions.
For example, the conf.design package is limited to non-commercial use, and
since I work for a for-profit business, I cannot use it.
I found out about the license terms of conf.design by chance; I would like to
avoid any possibility of a mistake in the future.
Is there some clever combination of grep and install.packages that I could use
to limit my downloads to, say, GPL-only packages?
Something like:
txt <- readLines(url("http://cran.r-project.org/web/packages/ALS/index.html";))
aok <- regexpr("GPL",txt[grep("License",txt)+1])>0
will work on CRAN as it is formatted now. Maybe roll it up in a function,
say license.ok(), that returns the name of package if aok or print the
license and stop if not aok. Then install.packages(license.ok(pkg.name))
should do it. Of course, this does not handle dependencies. For that you
might want to parse with index.html with XML, follow the dependencies and
check them all out, first.
HTH,
Chuck
Thanks,
Ted
Ted Mendum | Senior Scientist
Warner Babcock Institute for Green Chemistry
66 Cummings Park, Woburn, MA 01801
p: 781-937-9000
f:781-937-9001
[EMAIL PROTECTED]
www.warnerbabcock.com
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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Re: [R] Installing packages based on the license
On 26/11/2008 4:43 PM, Ted Mendum wrote: Hello, I would like have an automatic way to avoid installing packages that I cannot use due to license restrictions. For example, the conf.design package is limited to non-commercial use, and since I work for a for-profit business, I cannot use it. I found out about the license terms of conf.design by chance; I would like to avoid any possibility of a mistake in the future. Is there some clever combination of grep and install.packages that I could use to limit my downloads to, say, GPL-only packages? In theory, you should be able to look at the License field of available.packages(fields="License") and limit yourself to those with acceptable licenses. However, I don't think CRAN reports on the license. However, after you have installed a set of packages, you can scan the set of licenses using this code: installed.packages(fields="License")[,"License"] Duncan Murdoch Thanks, Ted Ted Mendum | Senior Scientist Warner Babcock Institute for Green Chemistry 66 Cummings Park, Woburn, MA 01801 p: 781-937-9000 f:781-937-9001 [EMAIL PROTECTED] www.warnerbabcock.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing packages on OS X -- lgfortran problem
I am trying to install two packages that are not available at CRAN (rmutil, dna). When trying the R CMD INSTALL with either file, I get an error message that ends with /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: can't locate file for: -lgfortran /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: file: -lgfortran is not an object file (not allowed in a library) Can anyone please help? I have R 2.6 on a Macbook running 10.4.10. I have installed XCode 2.5. A complete error message is given below. Thank you! Stefanie * Installing to library '/Library/Frameworks/R.framework/Resources/ library' * Installing *source* package 'rmutil' ... ** libs ** arch - i386 gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - msse3-fPIC -g -O2 -march=nocona -c cutil.c -o cutil.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - msse3-fPIC -g -O2 -march=nocona -c dist.c -o dist.o gfortran-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - fPIC -g -O2 -march=nocona -c gettvc.f -o gettvc.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - msse3-fPIC -g -O2 -march=nocona -c romberg.c -o romberg.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - msse3-fPIC -g -O2 -march=nocona -c toms614.c -o toms614.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,- macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module - multiply_defined suppress -o rmutil.so cutil.o dist.o gettvc.o romberg.o toms614.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.1 - lgfortran -lgcc_s.10.4 /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: can't locate file for: -lgfortran /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: file: -lgfortran is not an object file (not allowed in a library) make: *** [rmutil.so] Error 1 ERROR: compilation failed for package 'rmutil' ** Removing '/Library/Frameworks/R.framework/Versions/2.6/Resources/ library/rmutil' __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing Packages in Windows Vista -- YES I tried Run as Administrator
I'm having trouble installing packages in Windows Vista. It's driving me nuts. I read all the threads and I have tried the following: 1) Right click on R and Run as Administrator 2) Turn off User Account Control 3) Toss machine across room (OK haven't tried this one yet, but I'm close) Here is the R error messages I am getting --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.stat.ucla.edu/bin/windows/contrib/2.6/boot_1.2-32.zip' Content type 'application/zip' length 51 bytes (759 Kb) opened URL downloaded 32 Kb Error in gzfile(file, "r") : unable to open connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb") : downloaded length 33219 != reported length 51 2: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file 3: In gzfile(file, "r") : cannot open compressed file 'boot/DESCRIPTION', probable reason 'No such file or directory' Can anybody help? My presentation is in 14 hours and right now I'm thin on results. THANK YOU THANK YOU THANK YOU! -- Scotty -- View this message in context: http://www.nabble.com/Installing-Packages-in-Windows-VistaYES-I-tried-Run-as-Administrator-tp16993043p16993043.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Packages in Windows Vista -- YES I tried Run as Administrator
Your issue is a corrupt download. Try another CRAN mirror. In any case, the current version of R includes that version of boot, so you need to update (before posting, as the posting guide asked you to). On Thu, 1 May 2008, Scotty Nelson wrote: I'm having trouble installing packages in Windows Vista. It's driving me nuts. I read all the threads and I have tried the following: 1) Right click on R and Run as Administrator 2) Turn off User Account Control 3) Toss machine across room (OK haven't tried this one yet, but I'm close) Here is the R error messages I am getting --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.stat.ucla.edu/bin/windows/contrib/2.6/boot_1.2-32.zip' Content type 'application/zip' length 51 bytes (759 Kb) opened URL downloaded 32 Kb Error in gzfile(file, "r") : unable to open connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb") : downloaded length 33219 != reported length 51 ^ Did you not see that? 2: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file 3: In gzfile(file, "r") : cannot open compressed file 'boot/DESCRIPTION', probable reason 'No such file or directory' Can anybody help? My presentation is in 14 hours and right now I'm thin on results. THANK YOU THANK YOU THANK YOU! -- Scotty -- View this message in context: http://www.nabble.com/Installing-Packages-in-Windows-VistaYES-I-tried-Run-as-Administrator-tp16993043p16993043.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Packages in Windows Vista -- YES I tried Run as Administrator
Hi Scotty, Can't give an answer from what you've provided, but one temp. work-around that might work is to get onto CRAN -- packages and download the packages you need from your web browser as zip files, then do an "Install package(s) from local zip files..." from the Packages menu. HTH, Mark. Scotty Nelson wrote: > > I'm having trouble installing packages in Windows Vista. It's driving me > nuts. > I read all the threads and I have tried the following: > > 1) Right click on R and Run as Administrator > 2) Turn off User Account Control > 3) Toss machine across room (OK haven't tried this one yet, but I'm close) > > Here is the R error messages I am getting > > --- Please select a CRAN mirror for use in this session --- > trying URL > 'http://cran.stat.ucla.edu/bin/windows/contrib/2.6/boot_1.2-32.zip' > Content type 'application/zip' length 51 bytes (759 Kb) > opened URL > downloaded 32 Kb > > Error in gzfile(file, "r") : unable to open connection > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb") : > downloaded length 33219 != reported length 51 > 2: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file > 3: In gzfile(file, "r") : > cannot open compressed file 'boot/DESCRIPTION', probable reason 'No such > file or directory' > > Can anybody help? My presentation is in 14 hours and right now I'm thin > on results. > > THANK YOU THANK YOU THANK YOU! > > -- Scotty > -- View this message in context: http://www.nabble.com/Installing-Packages-in-Windows-VistaYES-I-tried-Run-as-Administrator-tp16993043p16995041.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
