Re: [R] Cannot Install Packages
On 10.05.2016 19:14, Jason Hernandez via R-help wrote:
I have been trying to install the package "reshape2" using the code:
install.packages("reshape2")
I get the following return:
Installing package into ‘C:/Users/Jason/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository
http://cran.cs.wwu.edu/bin/windows/contrib/3.0
The mirror does not exist, perhaps choose another one?
Best,
Uwe Ligges
Warning message:
package ‘reshape2’ is not available (for R version 3.0.2)
When I went to the list of packages to look up reshape2, it said this package
needs compilation. I did not see an indication of which R versions it is
available for.
I went to the R for Windows FAQ, but it did not seem very helpful. The relevant
sentences seemed to be:
"For packages with code that needscompilation you will need to collect and install
several tools: you candownload them via the portal
athttp://www.murdoch-sutherland.com/Rtools/. Once you have doneso, just run R CMD INSTALL
pkgname at a Windows commandprompt."
I did the download, but I do not understand the meaning of the last sentence, since R
does not recognize R CMD INSTALL as a valid code line, and the usual
install.packages("reshape2") still returns the same error. What did I miss?
Jason Hernandez
[[alternative HTML version deleted]]
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[R] Cannot Install Packages
I have been trying to install the package "reshape2" using the code:
> install.packages("reshape2")
I get the following return:
Installing package into ‘C:/Users/Jason/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository
http://cran.cs.wwu.edu/bin/windows/contrib/3.0
Warning message:
package ‘reshape2’ is not available (for R version 3.0.2)
When I went to the list of packages to look up reshape2, it said this package
needs compilation. I did not see an indication of which R versions it is
available for.
I went to the R for Windows FAQ, but it did not seem very helpful. The relevant
sentences seemed to be:
"For packages with code that needscompilation you will need to collect and
install several tools: you candownload them via the portal
athttp://www.murdoch-sutherland.com/Rtools/. Once you have doneso, just run R
CMD INSTALL pkgname at a Windows commandprompt."
I did the download, but I do not understand the meaning of the last sentence,
since R does not recognize R CMD INSTALL as a valid code line, and the usual
install.packages("reshape2") still returns the same error. What did I miss?
Jason Hernandez
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] Cannot install packages in R 2.12.0 on Windows 7
Thanks very much for your help. This was a case of some weird network card IP
reset hardware error that did something to permissions or something during the
install. Not exactly sure if this was part of the problem. But getting the
hardware corrected and reinstalling R 2.12.0 solved the problem. I'm filing
this under really obscure errors.
Cheers,
Dick
***
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
***
On Tue, 16 Nov 2010, Prof Brian Ripley wrote:
The error seems to be a BioC problem[*] and associated with having a package
installed with an empty DESCRIPTION file. So please take a look at your
installed packages and remove any such.
The following R code may help:
for(lib in .libPaths()) {
descs - Sys.glob(file.path(lib, *, DESCRIPTION))
sizes - file.info(descs)$size
names(sizes) - descs
print(sizes[sizes 100])
}
[*] They don't know how they did it, but reported this symptom on R-devel
recently.
On Mon, 15 Nov 2010, Dick Beyer wrote:
Hi,
I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are
the relevant lines:
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
source(http://www.bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(Biobase)
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] Biobase
Please wait...
Error: subscript out of bounds
traceback()
7: .readPkgDesc(lib, fields)
6: installed.packages(lib.loc = libpath, fields = c(Package, Version))
5: getDependencies(pkgs, dependencies, available, lib)
4: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
dependencies = dependencies, libs_only = libs_only, ...)
3: install.packages(pkgs = pkgs, repos = repos, ...) at biocinstall.R#205
2: biocinstall(pkgs = pkgs, groupName = groupName, ...) at biocLite.R#5
1: biocLite(Biobase)
It doesn't matter if I use biocLite, or just install.packages(), I get the
same error. I did a re-install of R, but that didn't help. I'm hoping
someone else has seen this error and might have a suggestion.
Thanks very much,
Dick
***
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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.
[R] Cannot install packages in R 2.12.0 on Windows 7
Hi, I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the relevant lines: sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base source(http://www.bioconductor.org/biocLite.R;) BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). biocLite(Biobase) Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] Biobase Please wait... Error: subscript out of bounds traceback() 7: .readPkgDesc(lib, fields) 6: installed.packages(lib.loc = libpath, fields = c(Package, Version)) 5: getDependencies(pkgs, dependencies, available, lib) 4: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, dependencies = dependencies, libs_only = libs_only, ...) 3: install.packages(pkgs = pkgs, repos = repos, ...) at biocinstall.R#205 2: biocinstall(pkgs = pkgs, groupName = groupName, ...) at biocLite.R#5 1: biocLite(Biobase) It doesn't matter if I use biocLite, or just install.packages(), I get the same error. I did a re-install of R, but that didn't help. I'm hoping someone else has seen this error and might have a suggestion. Thanks very much, Dick *** Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_bioinfo.html http://staff.washington.edu/~dbeyer __ 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] Cannot install packages in R 2.12.0 on Windows 7
The error seems to be a BioC problem[*] and associated with having a
package installed with an empty DESCRIPTION file. So please take a
look at your installed packages and remove any such.
The following R code may help:
for(lib in .libPaths()) {
descs - Sys.glob(file.path(lib, *, DESCRIPTION))
sizes - file.info(descs)$size
names(sizes) - descs
print(sizes[sizes 100])
}
[*] They don't know how they did it, but reported this symptom on
R-devel recently.
On Mon, 15 Nov 2010, Dick Beyer wrote:
Hi,
I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the
relevant lines:
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
source(http://www.bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(Biobase)
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] Biobase
Please wait...
Error: subscript out of bounds
traceback()
7: .readPkgDesc(lib, fields)
6: installed.packages(lib.loc = libpath, fields = c(Package, Version))
5: getDependencies(pkgs, dependencies, available, lib)
4: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
dependencies = dependencies, libs_only = libs_only, ...)
3: install.packages(pkgs = pkgs, repos = repos, ...) at biocinstall.R#205
2: biocinstall(pkgs = pkgs, groupName = groupName, ...) at biocLite.R#5
1: biocLite(Biobase)
It doesn't matter if I use biocLite, or just install.packages(), I get the same
error. I did a re-install of R, but that didn't help. I'm hoping someone else
has seen this error and might have a suggestion.
Thanks very much,
Dick
***
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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.
