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Question: unable to install qvalue..
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gravatar for Saurabh Bundela
6.8 years ago by
Saurabh Bundela30 wrote:
Hi, I am trying to install qvalue, however its giving installation error -> >>>> Error : package 'tcltk' does not have a name space ERROR: lazy loading failed for package ?qvalue? * removing ?/home/sbw/R/x86_64-unknown-linux-gnu-library/2.12/qvalue? The downloaded packages are in ?/tmp/RtmpKnS1X4/downloaded_packages? Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'qvalue' had non-zero exit status <<<< I even tried to install qvalue as well as tcltk2 packages from source, without any success. I am stuck... please help me in resolving this issue. Best Regards, Saurabh
ADD COMMENTlink modified 6.8 years ago by Martin Morgan ♦♦ 20k • written 6.8 years ago by Saurabh Bundela30
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gravatar for Martin Morgan
6.8 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
On 02/21/2011 04:36 AM, Saurabh Bundela wrote: > Hi, > > I am trying to install qvalue, however its giving installation error -> > >>>>> > Error : package 'tcltk' does not have a name space > ERROR: lazy loading failed for package ?qvalue? > * removing ?/home/sbw/R/x86_64-unknown-linux-gnu- library/2.12/qvalue? Hi Saurabh probably one or more of your packages are out of date. Try http://bioconductor.org/install/index.html#update-bioconductor- packages Provide sessionInfo() if this does not help. Martin > > The downloaded packages are in > ?/tmp/RtmpKnS1X4/downloaded_packages? > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'qvalue' had non-zero exit status > <<<< > > I even tried to install qvalue as well as tcltk2 packages from source, > without any success. > > I am stuck... please help me in resolving this issue. > > Best Regards, > > Saurabh > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 6.8 years ago by Martin Morgan ♦♦ 20k
Hi Martin, Saurabh, John On 02/21/2011 01:57 PM, Martin Morgan wrote: > On 02/21/2011 04:36 AM, Saurabh Bundela wrote: >> I am trying to install qvalue, however its giving installation error -> >> Error : package 'tcltk' does not have a name space > probably one or more of your packages are out of date. Try I also had problems with qvalue, and there is indeed something seriously wrong: The current version of 'qvalue' (v1.24.0 on CRAN, last changed 2010-10-26) depends on 'tcltk'. Now, if you look at CRAN's tcltk page, you get this here: "Package ?tcltk? was removed from the CRAN repository. Formerly available versions can be obtained from the archive." When did that happen? In October, it obviously was still around. The archive only lists a really old initial version. Could it be that the CRAN people deleted it accidentally? The 'tcltk2' package that the OP mentioned seems, by the way, not be a replacement of 'tcltk' but an add-on. It also lists 'tcltk' lists as one of its dependencies. A completely different question is why qvalue depends on tcltk. Does anybody actually use its GUI interface. To John Storey (CC'ed): What about moving this out of the package, or making it optional? (I.e., remove the dependency on tcltk from the DESCRIPTION file and instead try to load tcltk only if somebody calls the GUI function.) Cheers Simon +--- | Dr. Simon Anders, Dipl.-Phys. | European Molecular Biology Laboratory (EMBL), Heidelberg | office phone +49-6221-387-8632 | preferred (permanent) e-mail: sanders at fs.tum.de
ADD REPLYlink written 6.8 years ago by Simon Anders3.4k
Hi Simon, Check out this URL. http://www.tcl.tk/software/tcltk/ Various tcltk widgets are also available from http://sourceforge.net/. Use the search engine to locate tools such as BWidget, tcllib, tcltable etcetc. Dave Dr David Iles Institute for Integrative and Comparative Biology University of Leeds Leeds LS2 9JT d.e.iles at leeds.ac.uk On 21 Feb 2011, at 13:24, Simon Anders wrote: > Hi Martin, Saurabh, John > > On 02/21/2011 01:57 PM, Martin Morgan wrote: >> On 02/21/2011 04:36 AM, Saurabh Bundela wrote: >>> I am trying to install qvalue, however its giving installation error -> >>> Error : package 'tcltk' does not have a name space > >> probably one or more of your packages are out of date. Try > > I also had problems with qvalue, and there is indeed something seriously > wrong: > > The current version of 'qvalue' (v1.24.0 on CRAN, last changed > 2010-10-26) depends on 'tcltk'. > > Now, if you look at CRAN's tcltk page, you get this here: > > "Package ?tcltk? was removed from the CRAN repository. > Formerly available versions can be obtained from the archive." > > When did that happen? In October, it obviously was still around. The > archive only lists a really old initial version. Could it be that the > CRAN people deleted it accidentally? > > The 'tcltk2' package that the OP mentioned seems, by the way, not be a > replacement of 'tcltk' but an add-on. It also lists 'tcltk' lists as one > of its dependencies. > > > A completely different question is why qvalue depends on tcltk. Does > anybody actually use its GUI interface. To John Storey (CC'ed): What > about moving this out of the package, or making it optional? (I.e., > remove the dependency on tcltk from the DESCRIPTION file and instead try > to load tcltk only if somebody calls the GUI function.) > > Cheers > Simon > > > > > +--- > | Dr. Simon Anders, Dipl.-Phys. > | European Molecular Biology Laboratory (EMBL), Heidelberg > | office phone +49-6221-387-8632 > | preferred (permanent) e-mail: sanders at fs.tum.de > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.8 years ago by David Iles130
Hi David On 02/21/2011 02:44 PM, David Iles wrote: > Check out this URL. > > http://www.tcl.tk/software/tcltk/ > > Various tcltk widgets are also available from http://sourceforge.net/. Use the search engine to locate tools such as BWidget, tcllib, tcltable etcetc. Thanks, but I think, you misunderstood the issue. The CRAN package 'tcltk' is a set of R binding for Tcl/Tk, i.e. a package that allows you to use Tcl/Tk from within R. The issue is not that Tcl/Tk itself vanished from CRAN; it was never available there and users were always supposed to install Tcl/Tk on their system before attempting to import the 'tckltk' R package, which, as I said, is only a wrapper. And this wrapper is what has vanished from CRAN, which is an issue, because a large number of packages depend on it. Simon
ADD REPLYlink written 6.8 years ago by Simon Anders3.4k
At least in R 2.12, tcltk package source is in src/library of the source R distribution. There is no need to distribute it at CRAN AFAICT. On Mon, Feb 21, 2011 at 9:27 AM, Simon Anders <anders@embl.de> wrote: > Hi David > > > On 02/21/2011 02:44 PM, David Iles wrote: > >> Check out this URL. >> >> http://www.tcl.tk/software/tcltk/ >> >> Various tcltk widgets are also available from http://sourceforge.net/. >> Use the search engine to locate tools such as BWidget, tcllib, tcltable >> etcetc. >> > > Thanks, but I think, you misunderstood the issue. > > The CRAN package 'tcltk' is a set of R binding for Tcl/Tk, i.e. a package > that allows you to use Tcl/Tk from within R. The issue is not that Tcl/Tk > itself vanished from CRAN; it was never available there and users were > always supposed to install Tcl/Tk on their system before attempting to > import the 'tckltk' R package, which, as I said, is only a wrapper. > > And this wrapper is what has vanished from CRAN, which is an issue, because > a large number of packages depend on it. > > Simon > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Vincent J. Carey, Jr.6.2k
Hi Vince On 02/21/2011 04:05 PM, Vincent Carey wrote: > At least in R 2.12, tcltk package source is in src/library of the source > R distribution. There is no need to distribute it at CRAN AFAICT. Yes, this explains it. Sorry for missing this obvious point. I didn't have the 'tk-dev' package installed on my Ubuntu when I compiled my R, so it was skipped, and I guess this is also the original poster's problem. (Not wanting to compile all of R again, I just tried to install the tcltk package separately from my R source tree but that does not seem entirely straight-forward, because the Makefile in there need to be regenerated from the global configure script, and simply re-running does not do the job. Ok, I guess rebuilding everything is not a big deal and easiest.) The remaining issue is that the installation of 'qvalue' gives this misleading error message: Error : package 'tcltk' does not have a name space Other packages, e.g., 'tckltk2', properly report: Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error : package 'tcltk' could not be loaded But, I guess, the best would be if John dropped the dependency on 'qvalue'. I don't suppose that we should take for granted that the average user has Tk available. (Is it bundled to the R installer for Windows?) Simon
ADD REPLYlink written 6.8 years ago by Simon Anders3.4k
Hi Simon, On 2/21/2011 10:40 AM, Simon Anders wrote: > Hi Vince > > On 02/21/2011 04:05 PM, Vincent Carey wrote: >> At least in R 2.12, tcltk package source is in src/library of the source >> R distribution. There is no need to distribute it at CRAN AFAICT. > > Yes, this explains it. Sorry for missing this obvious point. > > > I didn't have the 'tk-dev' package installed on my Ubuntu when I > compiled my R, so it was skipped, and I guess this is also the original > poster's problem. > > (Not wanting to compile all of R again, I just tried to install the > tcltk package separately from my R source tree but that does not seem > entirely straight-forward, because the Makefile in there need to be > regenerated from the global configure script, and simply re-running does > not do the job. Ok, I guess rebuilding everything is not a big deal and > easiest.) > > > The remaining issue is that the installation of 'qvalue' gives this > misleading error message: > Error : package 'tcltk' does not have a name space > > Other packages, e.g., 'tckltk2', properly report: > > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error : package 'tcltk' could not be loaded > > > But, I guess, the best would be if John dropped the dependency on > 'qvalue'. I don't suppose that we should take for granted that the > average user has Tk available. (Is it bundled to the R installer for > Windows?) The tcltk package comes by default with the R installer on Windows, and for that matter on *nix as well. It is used by several of the base functions like install.packages(), and IMO can be considered at least on the level of a recommended package. John can do with his package as he likes, but I don't see a strong argument for dropping a dependency on a package that has such a high expectation of being installed. Best, Jim > > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 6.8 years ago by James W. MacDonald45k
On Mon, Feb 21, 2011 at 10:40 AM, Simon Anders <anders@embl.de> wrote: > Hi Vince > > > On 02/21/2011 04:05 PM, Vincent Carey wrote: > >> At least in R 2.12, tcltk package source is in src/library of the source >> R distribution. There is no need to distribute it at CRAN AFAICT. >> > > Yes, this explains it. Sorry for missing this obvious point. > > > I didn't have the 'tk-dev' package installed on my Ubuntu when I compiled > my R, so it was skipped, and I guess this is also the original poster's > problem. > > (Not wanting to compile all of R again, I just tried to install the tcltk > package separately from my R source tree but that does not seem entirely > straight-forward, because the Makefile in there need to be regenerated from > the global configure script, and simply re-running does not do the job. Ok, > I guess rebuilding everything is not a big deal and easiest.) > > > The remaining issue is that the installation of 'qvalue' gives this > misleading error message: > > Error : package 'tcltk' does not have a name space > > I think this is inevitable since qvalue only imports tcltk -- there is no need to attempt the load that generates the error you note below. Whether R should report that a package is not installed when an import is attempted but the package is not installed seems to be an issue for R-core. > Other packages, e.g., 'tckltk2', properly report: > > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error : package 'tcltk' could not be loaded > > > But, I guess, the best would be if John dropped the dependency on 'qvalue'. > I don't suppose that we should take for granted that the average user has Tk > available. (Is it bundled to the R installer for Windows?) > > I wouldn't be surprised if there is a sizable user segment that uses the widgets productively. So users are encouraged to get their tcltk infrastructure in order if they want the qvalue package. It isn't too hard. However, on my CentOs, after installing the infrastructure from source and setting the configure variables properly ... > capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE TRUE TRUE TRUE FALSE TRUE > library(qvalue) > help(package=qvalue) > qvalue.gui() Error in qvalue.gui() : could not find function "tclVar" # so is "Imports" enough? > library(tcltk) Loading Tcl/Tk interface ... done Warning message: In fun(...) : Can't find a usable tk.tcl in the following directories: /mnt/data/stvjc/ExternalSoft/TCL-DIST/lib/tcl8.5/tk8.5 /mnt/data/stvjc/ExternalSoft/TCL-DIST/lib/tk8.5 ./lib/tk8.5 ./library This probably means that tk wasn't installed properly. > qvalue.gui() <tcl> At this point the gui looks good, despite what R has said about improper installation ... but I am not pushing it further. Whether I will take this invitation to another half-hour of the interoperability blues is an open question ... > sessionInfo() R version 2.13.0 Under development (unstable) (2011-02-21 r54514) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] tcltk stats graphics grDevices datasets utils methods [8] base other attached packages: [1] qvalue_1.24.0 > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Vincent J. Carey, Jr.6.2k
Hi Simon, I have recently installed tcltk manually into R - you can then get R to use tcltk automatically from wherever the software is installed. Download the latest tcltk tar.gz file from sourceforge (check out http://sourceforge.net/projects/tcl/files/Tcl/) and unpack it, eg into the R library. >From the R prompt, check out where R is looking for tcltk with > tclvalue("auto_path") If where you have installed tcltk is missing from the list that appears, then add the path, for example: > addTclPath("/Users/Library/R/2.12/library") Hope that helps. Dave Dr David Iles Institute for Integrative and Comparative Biology University of Leeds Leeds LS2 9JT d.e.iles at leeds.ac.uk On 21 Feb 2011, at 14:27, Simon Anders wrote: > Hi David > > On 02/21/2011 02:44 PM, David Iles wrote: >> Check out this URL. >> >> http://www.tcl.tk/software/tcltk/ >> >> Various tcltk widgets are also available from http://sourceforge.net/. Use the search engine to locate tools such as BWidget, tcllib, tcltable etcetc. > > Thanks, but I think, you misunderstood the issue. > > The CRAN package 'tcltk' is a set of R binding for Tcl/Tk, i.e. a > package that allows you to use Tcl/Tk from within R. The issue is not > that Tcl/Tk itself vanished from CRAN; it was never available there and > users were always supposed to install Tcl/Tk on their system before > attempting to import the 'tckltk' R package, which, as I said, is only a > wrapper. > > And this wrapper is what has vanished from CRAN, which is an issue, > because a large number of packages depend on it. > > Simon
ADD REPLYlink written 6.8 years ago by David Iles130
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