Hi Khalid, Let's keep this on the Bioconductor list so others can contribute and learn. See below: On Tue, Oct 16, 2012 at 4:53 AM, Khalid EL KARKOURI <khalid.elkarkouri at="" univ-amu.fr=""> wrote: > Hi Dan, > > Please I need your help again ! > > I tried to install the package mcaGUI and have the followings: > >> source("http://bioconductor.org/biocLite.R") > > Bioconductor version 2.11 (BiocInstaller 1.8.2), ?biocLite for help >> >> biocLite("mcaGUI") > > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.2), R version 2.15. > Installing package(s) 'mcaGUI' > also installing the dependencies 'rgl', 'bpca' > > essai de l'URL 'http://cran.fhcrc.org/src/contrib/rgl_0.92.892.tar.gz' > Content type 'application/x-gzip' length 1713881 bytes (1.6 Mb) > URL ouverte > ================================================== > downloaded 1.6 Mb > > essai de l'URL 'http://cran.fhcrc.org/src/contrib/bpca_1.0-10.tar.gz' > Content type 'application/x-gzip' length 168473 bytes (164 Kb) > URL ouverte > ================================================== > downloaded 164 Kb > > essai de l'URL > 'http://bioconductor.org/packages/2.11/bioc/src/contrib/mcaGUI_1.6.0 .tar.gz' > Content type 'application/x-gzip' length 2266727 bytes (2.2 Mb) > URL ouverte > ================================================== > downloaded 2.2 Mb > > * installing *source* package 'rgl' ... > ** package 'rgl' correctement d?compress? et sommes MD5 v?rifi?es > checking for gcc... gcc -std=gnu99 > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for gcc... (cached) gcc -std=gnu99 > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc -std=gnu99 accepts -g... (cached) yes > checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed > checking for libpng-config... yes > configure: using libpng-config > configure: using libpng dynamic linkage > checking for X... libraries , headers > checking GL/gl.h usability... no > checking GL/gl.h presence... no > checking for GL/gl.h... no > checking GL/glu.h usability... no > checking GL/glu.h presence... no > checking for GL/glu.h... no > configure: error: missing required header GL/gl.h > ERROR: configuration failed for package 'rgl' What this is telling us is that mcaGUI depends on the CRAN package rgl, and if we look at the web page for that package: http://cran.r-project.org/web/packages/rgl/index.html we see this line: SystemRequirements: OpenGL, GLU Library, zlib (optional), libpng (>=1.2.9, optional), FreeType (optional) This means, these are system-level packages (not R packages) that R cannot install for you, but which need to be present. Sounds like you are using openSuSE. So if you can determine which packages contain these dependencies, then you can install them with yast2 or zypper. It looks like someone else has had a similar problem and a solution here: http://r.789695.n4.nabble.com/Installing-rgl-td865867.html Since rgl is a CRAN package, this is technically not a Bioconductor question. So you might want to ask on the R-help mailing list, and/or contact the rgl maintainer, whose email address is listed here: http://cran.r-project.org/web/packages/rgl/index.html Thanks, Dan > * removing '/usr/lib64/R/library/rgl' > ERROR: dependency 'rgl' is not available for package 'bpca' > * removing '/usr/lib64/R/library/bpca' > ERROR: dependency 'bpca' is not available for package 'mcaGUI' > * removing '/usr/lib64/R/library/mcaGUI' > > The downloaded source packages are in > '/tmp/RtmpT3UIsT/downloaded_packages' > Updating HTML index of packages in '.Library' > Making packages.html ... done > Old packages: 'AnnotationDbi', 'boot', 'class', 'cluster', 'foreign', > 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', > 'rpart', > 'spatial' > > Update all/some/none? [a/s/n]: n > Messages d'avis : > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'rgl' had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'bpca' had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'mcaGUI' had non-zero exit status > >> library("mcaGUI") > > Erreur dans library("mcaGUI") : aucun package nomm? 'mcaGUI' n'est trouv? >> >> > > > Many thanks for your help, > > Khalid > > > ----- Message de dtenenba at fhcrc.org --------- > Date : Mon, 15 Oct 2012 13:30:17 -0700 > De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > Objet : Re: [BioC] package grid > ? : Khalid EL KARKOURI <khalid.elkarkouri at="" univ-amu.fr=""> > Cc : bioconductor at r-project.org > > >> On Mon, Oct 15, 2012 at 9:12 AM, Khalid EL KARKOURI >> <khalid.elkarkouri at="" univ-amu.fr=""> wrote: >>> >>> Hi Dan, >>> Herein the session info (thanks a lot), >>> >>> >>>> sessionInfo() >>> >>> >>> R version 2.15.1 (2012-06-22) >>> Platform: x86_64-suse-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 >>> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >> >> >> >> Thanks, and can you send the exact output of the >> library(grid) >> command? >> >> If successful, it should not return anything, i.e., it will look like >> this: >> >>> library(grid) >>> >> >> But subsequently, grid will appear in the list of "attached base >> packages" when you run >> sessionInfo() >> >> Thanks, >> Dan >> >>> >>> >>> >>> >>> ----- Message de dtenenba at fhcrc.org --------- >>> Date : Mon, 15 Oct 2012 08:33:45 -0700 >>> >>> De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>> Objet : Re: [BioC] package grid >>> ? : Khalid EL KARKOURI <khalid.elkarkouri at="" univ-amu.fr=""> >>> Cc : bioconductor at r-project.org >>> >>> >>>> Hi Khalid, >>>> >>>> On Mon, Oct 15, 2012 at 7:26 AM, Khalid EL KARKOURI >>>> <khalid.elkarkouri at="" univ-amu.fr=""> wrote: >>>>> >>>>> >>>>> High Dan, >>>>> >>>>> Herein the session info: >>>>> >>>>>> install.packages("grid") >>>>> >>>>> >>>>> >>>>> --- SVP s?lectionner un miroir CRAN pour cette session --- >>>>> CRAN mirror >>>>> >>>>> 1: Argentina (La Plata) 2: Argentina (Mendoza) >>>>> 3: Australia (Canberra) 4: Australia (Melbourne) >>>>> 5: Austria 6: Belgium >>>>> 7: Brazil (PR) 8: Brazil (RJ) >>>>> 9: Brazil (SP 1) 10: Brazil (SP 2) >>>>> 11: Canada (BC) 12: Canada (NS) >>>>> 13: Canada (ON) 14: Canada (QC 1) >>>>> 15: Canada (QC 2) 16: Chile >>>>> 17: China (Beijing 1) 18: China (Beijing 2) >>>>> 19: China (Beijing 3) 20: China (Guangzhou) >>>>> 21: China (Hefei) 22: China (Xiamen) >>>>> 23: Colombia (Bogota) 24: Colombia (Cali) >>>>> 25: Denmark 26: Ecuador >>>>> 27: France (Lyon 1) 28: France (Lyon 2) >>>>> 29: Germany (Berlin) 30: Germany (Goettingen) >>>>> 31: Greece 32: Hungary >>>>> 33: India 34: Indonesia >>>>> 35: Iran 36: Ireland >>>>> 37: Italy (Milano) 38: Italy (Padua) >>>>> 39: Italy (Palermo) 40: Japan (Hyogo) >>>>> 41: Japan (Tsukuba) 42: Japan (Tokyo) >>>>> 43: Korea 44: Latvia >>>>> 45: Mexico (Mexico City) 46: Mexico (Texcoco) >>>>> 47: Netherlands (Amsterdam) 48: Netherlands (Utrecht) >>>>> 49: New Zealand 50: Norway >>>>> 51: Philippines 52: Poland (Wroclaw) >>>>> 53: Russia 54: Singapore >>>>> 55: Slovakia 56: South Africa >>>>> 57: Spain (Madrid) 58: Sweden >>>>> 59: Switzerland 60: Taiwan (Taichung) >>>>> 61: Taiwan (Taipei) 62: Thailand >>>>> 63: UK (Bristol) 64: UK (London) >>>>> 65: UK (St Andrews) 66: USA (CA 1) >>>>> 67: USA (CA 2) 68: USA (IA) >>>>> 69: USA (IN) 70: USA (KS) >>>>> 71: USA (MI) 72: USA (MO) >>>>> 73: USA (OH) 74: USA (OR) >>>>> 75: USA (PA 1) 76: USA (PA 2) >>>>> 77: USA (TN) 78: USA (TX 1) >>>>> 79: USA (WA 1) 80: USA (WA 2) >>>>> 81: Venezuela 82: Vietnam >>>>> >>>>> >>>>> S?lection : 27 >>>>> Message d'avis : >>>>> package 'grid' is not available (for R version 2.15.1) >>>>> >>>>> >>>>> >>>> >>>> Please enter the command: >>>> >>>> sessionInfo() >>>> >>>> at an R prompt and email us the output. It should look something like >>>> this: >>>> >>>>> sessionInfo() >>>> >>>> >>>> R version 2.15.1 (2012-06-22) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> Dan >>>> >>>> >>>>> >>>>> >>>>> Many thanks, >>>>> >>>>> >>>>> Khalid >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ----- Message de dtenenba at fhcrc.org --------- >>>>> Date : Mon, 15 Oct 2012 06:39:50 -0700 >>>>> >>>>> De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>>>> Objet : Re: [BioC] package grid >>>>> ? : Khalid EL KARKOURI <khalid.elkarkouri at="" univ-amu.fr=""> >>>>> Cc : bioconductor at r-project.org, kasperdanielhansen at gmail.com >>>>> >>>>> >>>>> >>>>>> Please send the output of sessionInfo(). >>>>>> Dan >>>>>> >>>>>> >>>>>> On Mon, Oct 15, 2012 at 1:42 AM, Khalid EL KARKOURI >>>>>> <khalid.elkarkouri at="" univ-amu.fr=""> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> Dear All, >>>>>>> >>>>>>> Thank you very much for your answers. I used each one but it did not >>>>>>> works. >>>>>>> >>>>>>> install.packages("grid") doesn't work (the package is not available >>>>>>> for >>>>>>> R >>>>>>> 2.15.1) >>>>>>> >>>>>>> library(grid) : doesn't work (the library doesn't exist >>>>>>> >>>>>>> >>>>>>> Thank you for your help, >>>>>>> >>>>>>> >>>>>>> Khalid >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Message de dtenenba at fhcrc.org --------- >>>>>>> Date : Sat, 13 Oct 2012 10:15:12 -0700 >>>>>>> De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>>>>>> Objet : Re: [BioC] package grid >>>>>>> ? : Khalid EL KARKOURI <khalid.elkarkouri at="" univ-="" amu.fr=""> >>>>>>> Cc : bioconductor at r-project.org >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Fri, Oct 12, 2012 at 5:24 AM, Khalid EL KARKOURI >>>>>>>> <khalid.elkarkouri at="" univ-amu.fr=""> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Dear All, >>>>>>>>> >>>>>>>>> I have installed the R version 2.15.1 and wanted to install the >>>>>>>>> package >>>>>>>>> grid: The answer was the package is not available for that verion. >>>>>>>>> >>>>>>>>> Could you please give any help ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> This is really a question for R-help >>>>>>>> (http://stat.ethz.ch/mailman/listinfo/r-help) because grid is not a >>>>>>>> bioconductor package. >>>>>>>> >>>>>>>> However, the answer is: >>>>>>>> install.packages("grid") >>>>>>>> >>>>>>>> Dan >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> thank you >>>>>>>>> >>>>>>>>> Khalid >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Khalid EL KARKOURI >>>>>>>>> Aix-Marseille-Universit? >>>>>>>>> http://annuaire.univmed.fr/showuser.php?uid=el-karkour.k >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Fin du message de dtenenba at fhcrc.org ----- >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Khalid EL KARKOURI >>>>>>> Aix-Marseille-Universit? >>>>>>> http://annuaire.univmed.fr/showuser.php?uid=el-karkour.k >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> ----- Fin du message de dtenenba at fhcrc.org ----- >>>>> >>>>> >>>>> -- >>>>> >>>>> Khalid EL KARKOURI >>>>> Aix-Marseille-Universit? >>>>> http://annuaire.univmed.fr/showuser.php?uid=el-karkour.k >>>> >>>> >>>> >>> >>> >>> ----- Fin du message de dtenenba at fhcrc.org ----- >>> >>> >>> -- >>> >>> Khalid EL KARKOURI >>> Aix-Marseille-Universit? >>> http://annuaire.univmed.fr/showuser.php?uid=el-karkour.k >> >> > > > ----- Fin du message de dtenenba at fhcrc.org ----- > > > > -- > > Khalid EL KARKOURI > Aix-Marseille-Universit? > http://annuaire.univmed.fr/showuser.php?uid=el-karkour.k