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Question: Installing packages
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gravatar for Rohmatul Fajriyah
4.9 years ago by
Rohmatul Fajriyah190 wrote:
Dear All, I recently tried to use the Biconductor Cloud AMI (RStudio). I installed some packages and it was ok. Then I installed the "gsl", "Rcmdr" and "MBCB"packages and it was not ok. For the "Rcmdr" and "MBCB", the message was: Warning in fun(libname, pkgname) : couldn't connect to display ":0" For the "gsl", the message was: Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help * installing *source* package ‘gsl’ ... ** package ‘gsl’ successfully unpacked and MD5 sums checked checking for gsl-config... no configure: error: gsl-config not found, is GSL installed? ERROR: configuration failed for package ‘gsl’ * removing ‘/home/ubuntu/R/library/gsl’ Warning in install.packages :   installation of package ‘gsl’ had non-zero exit status Here for the sessionInfo() > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C           LC_COLLATE=C         [5] LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C          LC_NAME=C            [9] LC_ADDRESS=C         LC_TELEPHONE=C      LC_MEASUREMENT=C     LC_IDENTIFICATION=C attached base packages: [1] tcltk     stats     graphics  grDevices utils     datasets  methods   base     other attached packages:  [1] NormalGamma_0.1.0   histogram_0.0-23    optimx_2012.04.01  numDeriv_2012.9-1   [5] car_2.0-15          nnet_7.3-4          MASS_7.3-21        ffpe_1.2.0          [9] TTR_0.21-1          xts_0.8-8           zoo_1.7-7          lumi_2.10.0        [13] nleqslv_1.9.4       affy_1.36.0         Biobase_2.18.0     BiocGenerics_0.4.0 [17] MBCB_1.12.0         tcltk2_1.2-3        BiocInstaller_1.8.3 loaded via a namespace (and not attached):  [1] AnnotationDbi_1.20.0  DBI_0.2-5            IRanges_1.16.2        [4] KernSmooth_2.23-8     Matrix_1.0-9          RSQLite_0.11.2        [7] XML_3.95-0.1          affyio_1.26.0        annotate_1.36.0      [10] colorspace_1.1-1      grid_2.15.1          lattice_0.20-10      [13] methylumi_2.4.0       mgcv_1.7-21           nlme_3.1-104         [16] parallel_2.15.1       preprocessCore_1.20.0 sfsmisc_1.0-23      [19] stats4_2.15.1         tools_2.15.1          xtable_1.7-0         [22] zlibbioc_1.4.0 Any help, is really appreciated,  please ... Thank you very much. With kind regards, R Fajriyah (as far as I am concerned, I am not a member of this group yet) [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.9 years ago by Dan Tenenbaum60 • written 4.9 years ago by Rohmatul Fajriyah190
0
gravatar for Dan Tenenbaum
4.9 years ago by
United States
Dan Tenenbaum60 wrote:
Rohmatul Fajriyah wrote: > Dear All, > > I recently tried to use the Biconductor Cloud AMI (RStudio). > > I installed some packages and it was ok. > Then I installed the "gsl", "Rcmdr" and "MBCB"packages and it was not ok. > > For the "Rcmdr" and "MBCB", the message was: > Warning in fun(libname, pkgname) : couldn't connect to display ":0" > Rcmdr will not work under Rstudio Server. They use different GUI paradigms. > > For the "gsl", the message was: > > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > * installing *source* package ???gsl??? ... > ** package ???gsl??? successfully unpacked and MD5 sums checked > checking for gsl-config... no > configure: error: gsl-config not found, is GSL installed? > ERROR: configuration failed for package ???gsl??? > * removing ???/home/ubuntu/R/library/gsl??? > Warning in install.packages : > ? installation of package ???gsl??? had non-zero exit status > > Here for the sessionInfo() > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > ? [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C ? ? ? ? LC_TIME=C ? ? ? ? ? ? LC_COLLATE=C ? ? ? ? > ? [5] LC_MONETARY=C ? ? ? ? LC_MESSAGES=C ? ? ? ? LC_PAPER=C ? ? ? ? ? LC_NAME=C ? ? ? ? ? ? > ? [9] LC_ADDRESS=C ? ? ? ? LC_TELEPHONE=C ? ? ? LC_MEASUREMENT=C ? ? LC_IDENTIFICATION=C? > > attached base packages: > [1] tcltk ? ? stats ? ? graphics ? grDevices utils ? ? datasets ? methods ? base ? ? ? > > other attached packages: > ? [1] NormalGamma_0.1.0 ? histogram_0.0-23 ? ? optimx_2012.04.01 ? numDeriv_2012.9-1 ? > ? [5] car_2.0-15 ? ? ? ? ? nnet_7.3-4 ? ? ? ? ? MASS_7.3-21 ? ? ? ? ffpe_1.2.0 ? ? ? ? ? > ? [9] TTR_0.21-1 ? ? ? ? ? xts_0.8-8 ? ? ? ? ? zoo_1.7-7 ? ? ? ? ? lumi_2.10.0 ? ? ? ? > [13] nleqslv_1.9.4 ? ? ? affy_1.36.0 ? ? ? ? Biobase_2.18.0 ? ? ? BiocGenerics_0.4.0? > [17] MBCB_1.12.0 ? ? ? ? tcltk2_1.2-3 ? ? ? ? BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > ? [1] AnnotationDbi_1.20.0 ? DBI_0.2-5 ? ? ? ? ? ? IRanges_1.16.2 ? ? ? ? > ? [4] KernSmooth_2.23-8 ? ? Matrix_1.0-9 ? ? ? ? ? RSQLite_0.11.2 ? ? ? ? > ? [7] XML_3.95-0.1 ? ? ? ? ? affyio_1.26.0 ? ? ? ? annotate_1.36.0 ? ? ? > [10] colorspace_1.1-1 ? ? ? grid_2.15.1 ? ? ? ? ? lattice_0.20-10 ? ? ? > [13] methylumi_2.4.0 ? ? ? mgcv_1.7-21 ? ? ? ? ? nlme_3.1-104 ? ? ? ? ? > [16] parallel_2.15.1 ? ? ? preprocessCore_1.20.0 sfsmisc_1.0-23 ? ? ? ? > [19] stats4_2.15.1 ? ? ? ? tools_2.15.1 ? ? ? ? ? xtable_1.7-0 ? ? ? ? ? > [22] zlibbioc_1.4.0? > I have now installed gsl on the BioC 2.11 AMI, so if you start a new instance, this package should be installed. Dan > Any help, is really appreciated, ? please ... > > Thank you very much. > > With kind regards, > R Fajriyah > (as far as I am concerned, I am not a member of this group yet) > > [[alternative HTML version deleted]] >
ADD COMMENTlink written 4.9 years ago by Dan Tenenbaum60
Dear Dan and Steve, Thank you very much for your respond and I find that it will help me. Thanks! With kind regards, R Fajriyah ________________________________ From: Dan Tenenbaum <dandante@dandante.com> ct.org> Sent: Friday, December 28, 2012 9:03 PM Subject: Re: [BioC] Installing packages Rohmatul Fajriyah wrote: > Dear All, > > I recently tried to use the Biconductor Cloud AMI (RStudio). > > I installed some packages and it was ok. > Then I installed the "gsl", "Rcmdr" and "MBCB"packages and it was not ok. > > For the "Rcmdr" and "MBCB", the message was: > Warning in fun(libname, pkgname) : couldn't connect to display ":0" > Rcmdr will not work under Rstudio Server. They use different GUI paradigms. > > For the "gsl", the message was: > > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > * installing *source* package ‘gsl’ ... > ** package ‘gsl’ successfully unpacked and MD5 sums checked > checking for gsl-config... no > configure: error: gsl-config not found, is GSL installed? > ERROR: configuration failed for package ‘gsl’ > * removing ‘/home/ubuntu/R/library/gsl’ > Warning in install.packages : >   installation of package ‘gsl’ had non-zero exit status > > Here for the sessionInfo() > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: >  [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C        LC_TIME=C            LC_COLLATE=C        >  [5] LC_MONETARY=C        LC_MESSAGES=C       LC_PAPER=C           LC_NAME=C          >  [9] LC_ADDRESS=C         LC_TELEPHONE=C      LC_MEASUREMENT=C     LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk     stats     graphics  grDevices utils    datasets  methods   base     > > other attached packages: >  [1] NormalGamma_0.1.0   histogram_0.0-23    optimx_2012.04.01   numDeriv_2012.9-1  >  [5] car_2.0-15          nnet_7.3-4         MASS_7.3-21         ffpe_1.2.0         >  [9] TTR_0.21-1          xts_0.8-8          zoo_1.7-7           lumi_2.10.0       > [13] nleqslv_1.9.4       affy_1.36.0        Biobase_2.18.0      BiocGenerics_0.4.0 > [17] MBCB_1.12.0         tcltk2_1.2-3        BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): >  [1] AnnotationDbi_1.20.0  DBI_0.2-5            IRanges_1.16.2       >  [4] KernSmooth_2.23-8     Matrix_1.0-9         RSQLite_0.11.2       >  [7] XML_3.95-0.1          affyio_1.26.0        annotate_1.36.0      > [10] colorspace_1.1-1      grid_2.15.1          lattice_0.20-10      > [13] methylumi_2.4.0       mgcv_1.7-21          nlme_3.1-104         > [16] parallel_2.15.1       preprocessCore_1.20.0 sfsmisc_1.0-23       > [19] stats4_2.15.1         tools_2.15.1         xtable_1.7-0         > [22] zlibbioc_1.4.0 > I have now installed gsl on the BioC 2.11 AMI, so if you start a new instance, this package should be installed. Dan > Any help, is really appreciated,  please ... > > Thank you very much. > > With kind regards, > R Fajriyah > (as far as I am concerned, I am not a member of this group yet) > >    [[alternative HTML version deleted]] > [[alternative HTML version deleted]]
ADD REPLYlink written 4.9 years ago by Rohmatul Fajriyah190
0
gravatar for Steve Lianoglou
4.9 years ago by
Genentech
Steve Lianoglou12k wrote:
Hi, On Fri, Dec 28, 2012 at 6:20 AM, Rohmatul Fajriyah <rfajriyah at="" yahoo.com=""> wrote: > Dear All, > > I recently tried to use the Biconductor Cloud AMI (RStudio). > > I installed some packages and it was ok. > Then I installed the "gsl", "Rcmdr" and "MBCB"packages and it was not ok. > > For the "Rcmdr" and "MBCB", the message was: > Warning in fun(libname, pkgname) : couldn't connect to display ":0" By looking at the requirements for these packages, I see that they both require "gui components", ie. they both requires tcl/tk. These simply won't work on an Rstudio/web system ... Rstudio is creating a gui using http/web "stuff" that you then access through your web browser. For the tcl/tk stuff to work, I suspect you'll need an X11 client/server setup which is not this. So -- I don't expect there to be a fix for that. > For the "gsl", the message was: It's possible for a fix to this -- the AMI that the Bioc folks are using needs to have the GSL installed on it. Once that's done, this should be able to be installed (assuming they agree to add it, that is). > With kind regards, > R Fajriyah > (as far as I am concerned, I am not a member of this group yet) Huh? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 4.9 years ago by Steve Lianoglou12k
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