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Question: EBImage installation problem on Linux
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6.2 years ago by
Guest User12k
Guest User12k wrote:
Hi Group, I am trying to install the EBImage package on my linux box. I have the latest version of Red Hat Linux, GTK 2.10.4 and Image magick. The error which I get is as follows...Could anyone give me an idea what I am doing wrong? Please find the error message and session info below. I have already read an earlier post regarding the same issue (https://stat.ethz.ch/pipermail/bioconductor/2009-July/028666.html) and seen the response but I using latest version anyway. Thanks in advance. Jayangshu -- output of sessionInfo(): [root at CS-ORIS-SVR09 local]# R CMD INSTALL EBImage_3.12.0.tar.gz * installing to library ??/usr/local/lib64/R/library?? * installing *source* package ??EBImage?? ... checking for Magick-config... no configure: error: "ImageMagick or ImageMagick includes not found!" ERROR: configuration failed for package ??EBImage?? * removing ??/usr/local/lib64/R/library/EBImage?? [root at CS-ORIS-SVR09 local]# R R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.7, ?biocLite for help > biocLite("EBImage") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.7. Installing package(s) 'EBImage' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib /EBImage_3.12.0.tar.gz' Content type 'application/x-gzip' length 4738660 bytes (4.5 Mb) opened URL ================================================== downloaded 4.5 Mb * installing *source* package ??EBImage?? ... checking for Magick-config... no configure: error: "ImageMagick or ImageMagick includes not found!" ERROR: configuration failed for package ??EBImage?? * removing ??/usr/local/lib64/R/library/EBImage?? The downloaded source packages are in ??/tmp/Rtmpp42hTM/downloaded_packages?? Updating HTML index of packages in '.Library' Making packages.html ... done Old packages: 'caTools', 'gplots', 'gregmisc', 'RCurl' Update all/some/none? [a/s/n]: > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] tools_2.15.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 6.2 years ago by Wolfgang Huber13k • written 6.2 years ago by Guest User12k
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gravatar for Wolfgang Huber
6.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Jayangshu what happens when you type "Magick-config" in the command line? It appears that it is not installed, or if it is installed, that PATH and/or other environment variables are not set. If this sounds confusing to you, then perhaps you would best consult a Linux administrator. Please do follow the installation instructions in the PDF file that comes with the EBImage package. They are there for a reason. Btw, it is not advisable to run R CMD INSTALL as 'root' user. Better to create a user-id with restricted rights that can install R and R packages. Best wishes Wolfgang On 7/11/12 11:21 AM, Jayangshu Saha [guest] wrote: > > Hi Group, > > I am trying to install the EBImage package on my linux box. I have the latest version of Red Hat Linux, GTK 2.10.4 and Image magick. The error which I get is as follows...Could anyone give me an idea what I am doing wrong? > Please find the error message and session info below. > > I have already read an earlier post regarding the same issue (https://stat.ethz.ch/pipermail/bioconductor/2009-July/028666.html) and seen the response but I using latest version anyway. > > > Thanks in advance. > > Jayangshu > > -- output of sessionInfo(): > > [root at CS-ORIS-SVR09 local]# R CMD INSTALL EBImage_3.12.0.tar.gz > * installing to library ??/usr/local/lib64/R/library?? > * installing *source* package ??EBImage?? ... > checking for Magick-config... no > configure: error: "ImageMagick or ImageMagick includes not found!" > ERROR: configuration failed for package ??EBImage?? > * removing ??/usr/local/lib64/R/library/EBImage?? > > [root at CS-ORIS-SVR09 local]# R > > R version 2.15.0 (2012-03-30) > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.4.7, ?biocLite for help >> biocLite("EBImage") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.7. > Installing package(s) 'EBImage' > trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contr ib/EBImage_3.12.0.tar.gz' > Content type 'application/x-gzip' length 4738660 bytes (4.5 Mb) > opened URL > ================================================== > downloaded 4.5 Mb > > * installing *source* package ??EBImage?? ... > checking for Magick-config... no > configure: error: "ImageMagick or ImageMagick includes not found!" > ERROR: configuration failed for package ??EBImage?? > * removing ??/usr/local/lib64/R/library/EBImage?? > > The downloaded source packages are in > ??/tmp/Rtmpp42hTM/downloaded_packages?? > Updating HTML index of packages in '.Library' > Making packages.html ... done > Old packages: 'caTools', 'gplots', 'gregmisc', 'RCurl' > Update all/some/none? [a/s/n]: > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.4.7 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 6.2 years ago by Wolfgang Huber13k
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