Dear all,
How can a user install a package from BioC devel?
I have tried the following:
1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
Warning message:
package 'xps_0.4.1.tar.gz' is not available
3. download the package and use install.package locally:
> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.1
Best regards
Christian
_._._._._._._._._._._._._._._._
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l: cstrato at aon.at
_._._._._._._._._._._._._._._._
[Bioc-devel] How to install a package from bioC devel?
11 messages · Vincent Carey, cstrato, Oleg Sklyar +1 more
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu
On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
Warning message:
package 'xps_0.4.1.tar.gz' is not available
3. download the package and use install.package locally:
> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information transmitted in this electronic communica...{{dropped:9}}
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian
Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
Warning message:
package 'xps_0.4.1.tar.gz' is not available
3. download the package and use install.package locally:
> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information transmitted in this electronic communi...{{dropped:13}}
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian
Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
Warning message:
package 'xps_0.4.1.tar.gz' is not available
3. download the package and use install.package locally:
> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information transmitted in this electronic communi...{{dropped:13}}
Go to the bioconductor web page, download the package, and all the dependencies if required and save them onto a local disk. Then in Linux/UNIX/Mac do 'R CMD INSTALL ThePackage.tar.gz' outside of the R session and in Windows within an R session select in menu 'Install from a local Zip file'. However, please pay attention that those packages might be unsupported, not fully tested and even buggy - they are the development versions. So if you then encounter problems, be warned. Best, Oleg
cstrato wrote:
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
Warning message:
package 'xps_0.4.1.tar.gz' is not available
3. download the package and use install.package locally:
> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information transmitted in this electronic communi...{{dropped:13}}
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466
cstrato wrote:
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
First, you don't want to state the version. By giving the repository you will automatically get the correct version.
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
The above should have given you a big hint: What you gave as the repository ended up with 'bin/macosx/universal/contrib/2.6' added on the end. So two things are happening. First, the repository you are giving is wrong -- install.packages() will add the specific directory to get the package, so remove the src/contrib/ from the end. Second, you evidently want a source package, but you are not telling install.packages(), so it is trying to get the universal binary. Hint: type="source". Best, Jim
Warning message: package 'xps_0.4.1.tar.gz' is not available 3. download the package and use install.package locally:
> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information transmitted in this electronic communi...{{dropped:13}}
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
Dear Oleg As mentioned in my original mail, R CMD INSTALL is the ONLY method that worked for me! However, I want to know why install.packages() does not work, neither from an URL nor locally. Why does install.packages() not work? What is the correct url to access a package from BioC devel? Best regards Christian
Oleg Sklyar wrote:
Go to the bioconductor web page, download the package, and all the dependencies if required and save them onto a local disk. Then in Linux/UNIX/Mac do 'R CMD INSTALL ThePackage.tar.gz' outside of the R session and in Windows within an R session select in menu 'Install from a local Zip file'. However, please pay attention that those packages might be unsupported, not fully tested and even buggy - they are the development versions. So if you then encounter problems, be warned. Best, Oleg cstrato wrote:
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
Warning message:
package 'xps_0.4.1.tar.gz' is not available
3. download the package and use install.package locally:
>
install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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Dear Jim
Thank you very much, this is what I wanted to know. The following now works:
install.packages("xps",repos="http://www.bioconductor.org/packages/2.2/bioc",type="source")
Best regards
Christian
James W. MacDonald wrote:
cstrato wrote:
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
First, you don't want to state the version. By giving the repository you will automatically get the correct version.
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
The above should have given you a big hint: What you gave as the repository ended up with 'bin/macosx/universal/contrib/2.6' added on the end. So two things are happening. First, the repository you are giving is wrong -- install.packages() will add the specific directory to get the package, so remove the src/contrib/ from the end. Second, you evidently want a source package, but you are not telling install.packages(), so it is trying to get the universal binary. Hint: type="source". Best, Jim
Warning message: package 'xps_0.4.1.tar.gz' is not available 3. download the package and use install.package locally:
>
install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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Note that you might also want to add dependencies=TRUE. Best, Jim
cstrato wrote:
Dear Jim
Thank you very much, this is what I wanted to know. The following now
works:
install.packages("xps",repos="http://www.bioconductor.org/packages/2.2/bioc",type="source")
Best regards
Christian
James W. MacDonald wrote:
cstrato wrote:
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
First, you don't want to state the version. By giving the repository you will automatically get the correct version.
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
The above should have given you a big hint: What you gave as the repository ended up with 'bin/macosx/universal/contrib/2.6' added on the end. So two things are happening. First, the repository you are giving is wrong -- install.packages() will add the specific directory to get the package, so remove the src/contrib/ from the end. Second, you evidently want a source package, but you are not telling install.packages(), so it is trying to get the universal binary. Hint: type="source". Best, Jim
Warning message: package 'xps_0.4.1.tar.gz' is not available 3. download the package and use install.package locally:
>
install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
Thank you, I keep this in mind for the future. In my case I simply wanted to know if my package works as expected when a user downloads it. Best regards Christian
James W. MacDonald wrote:
Note that you might also want to add dependencies=TRUE. Best, Jim cstrato wrote:
Dear Jim
Thank you very much, this is what I wanted to know. The following now
works:
install.packages("xps",repos="http://www.bioconductor.org/packages/2.2/bioc",type="source")
Best regards
Christian
James W. MacDonald wrote:
cstrato wrote:
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos,
dependencies =
dependencies, :
argument 'lib' is missing: using
'/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps'
is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
First, you don't want to state the version. By giving the repository you will automatically get the correct version.
Warning in install.packages("xps_0.4.1.tar.gz", repos =
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
argument 'lib' is missing: using
'/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
The above should have given you a big hint: What you gave as the repository ended up with 'bin/macosx/universal/contrib/2.6' added on the end. So two things are happening. First, the repository you are giving is wrong -- install.packages() will add the specific directory to get the package, so remove the src/contrib/ from the end. Second, you evidently want a source package, but you are not telling install.packages(), so it is trying to get the universal binary. Hint: type="source". Best, Jim
Warning message: package 'xps_0.4.1.tar.gz' is not available 3. download the package and use install.package locally:
>
install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in
install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
repos = NULL) :
argument 'lib' is missing: using
'/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?
The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
> sessionInfo()
R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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communi...{{dropped:13}}
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1.
I see that this can be done, but I hope it is clear that we only test
packages from BioC devel on R-devel. There is no testing to verify that
a package from the devel branch will run on R-patched. It is possible
that a package in the devel branch will use a facility of R-devel that is
not present in R-patched. Cross-branch installation must be undertaken
with care.
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