EBImage_2.6.0/R2.8.1 installation problems
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Bernd Jagla ▴ 40
@bernd-jagla-3411
Last seen 18 months ago
Hi, I want to use the EBImage package but when trying to access/display an image I get the following error message. EBImage has never worked and this is the first time I am trying to use this package. Please let me know what else I can try to make it work? Here is the R output: R version 2.8.1 (2008-12-22) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 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. [Previously saved workspace restored] > library(EBImage) > f=system.file("images","lena.gif", package="EBImage") > lena=readImage(f) Warning message: In .DoCall("lib_readImages", as.character(files), as.integer(colormode)) : requested image not found or could not be loaded additional information: > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] EBImage_2.6.0 > Gtk information: pkg-config --cflags gtk+-2.0 -mms-bitfields -Ic:/gtk/include/gtk-2.0 -Ic:/gtk/lib/gtk-2.0/include -Ic:/gtk/include/atk-1.0 -Ic:/gtk/include/cairo -Ic:/gtk/include/p ango-1.0 -Ic:/gtk/include/glib-2.0 -Ic:/gtk/lib/glib-2.0/include -Ic:/gtk/include/libpng12 (GTK+-bundle2.16.0-20090317_win32) ImageMagick: ImageMagick 6.5.1 Q16 (dll version) When trying to open some tif files I get the following error message: IMDisplayDoc function (DoReadImage) reported a warning. Imdisplay.exe: Compression algorithm does not support random access. (.) tiff.c/TIFFErrors/324 Gifs, miff, PNG I can open. But eventually I am actually interested in opening TIFF files . Thanks for your kind help, Bernd Bernd Jagla Bioinformatician Institute Pasteur Plate-forme puces a ADN Genopole / Institut Pasteur 28 rue du Docteur Roux 75724 Paris Cedex 15 France <mailto:bernd.jagla@pasteur.fr> bernd.jagla@pasteur.fr tel: <http: www.plaxo.com="" click_to_call?lang="en&amp;src=jj_signature&amp;To=%2B33+" %280%2="" 9+140+61+35+13&email="berndjagla@yahoo.com"> +33 (0) 140 61 35 13 [[alternative HTML version deleted]]
EBImage EBImage • 977 views
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Gregoire Pau ▴ 30
@gregoire-pau-3182
Last seen 7.7 years ago
Hi Bernd, First, I would suggest you to switch to the latest Bioconductor release 2.4, which contains EBImage 3.0.0 (also available at http://bioconductor.org/packages/2.4/bioc/html/EBImage.html). EBImage 3.0.0 is a major release which fixes a lot of speed/bug/design issues. Reading/displaying an image is easy: > library(EBImage) > f = system.file("images","lena.gif", package="EBImage") > lena = readImage(f) > display(lena) EBImage relies on ImageMagick to read images, which itself relies on libtiff to decipher the TIFF format. Some TIFF images can contain private sections, undefined in the TIFF 6.0 specification, causing troubles to libtiff when reading (these sections are sometimes deliberately used to prevent file exchange). Please check first if you can display the images with ImageMagick 'display' command. If not, I would suggest to either update your libtiff library, or to save your images or convert them using the software provided with your microscope into a more portable lossless format (PNG, BMP, TGA...). Best regards, Greg --- Gregoire Pau EMBL Research officer http://www.ebi.ac.uk/~gpau/ Bernd Jagla wrote: > Hi, > > > > I want to use the EBImage package but when trying to access/display an image > I get the following error message. > > EBImage has never worked and this is the first time I am trying to use this > package. > > Please let me know what else I can try to make it work? > > > > > > Here is the R output: > > > > R version 2.8.1 (2008-12-22) > > Copyright (C) 2008 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > > > 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. > > > > [Previously saved workspace restored] > > > >> library(EBImage) > >> f=system.file("images","lena.gif", package="EBImage") > >> lena=readImage(f) > > Warning message: > > In .DoCall("lib_readImages", as.character(files), as.integer(colormode)) : > > requested image not found or could not be loaded > > > > additional information: > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] EBImage_2.6.0 > > > > > Gtk information: > > > > pkg-config --cflags gtk+-2.0 > > -mms-bitfields -Ic:/gtk/include/gtk-2.0 -Ic:/gtk/lib/gtk-2.0/include > -Ic:/gtk/include/atk-1.0 -Ic:/gtk/include/cairo -Ic:/gtk/include/p > > ango-1.0 -Ic:/gtk/include/glib-2.0 -Ic:/gtk/lib/glib-2.0/include > -Ic:/gtk/include/libpng12 > > > > (GTK+-bundle2.16.0-20090317_win32) > > > > ImageMagick: > > ImageMagick 6.5.1 Q16 (dll version) > > > > When trying to open some tif files I get the following error message: > > IMDisplayDoc function (DoReadImage) reported a warning. > > Imdisplay.exe: Compression algorithm does not support random access. (.) > tiff.c/TIFFErrors/324 > > Gifs, miff, PNG I can open. > > > > But eventually I am actually interested in opening TIFF files . > > > > > > Thanks for your kind help, > > > > > > Bernd > > > > > > > > > > Bernd Jagla > Bioinformatician > > Institute Pasteur > Plate-forme puces a ADN > Genopole / Institut Pasteur > 28 rue du Docteur Roux > 75724 Paris Cedex 15 > France > > > <mailto:bernd.jagla at="" pasteur.fr=""> bernd.jagla at pasteur.fr > > > tel: > > > <http: www.plaxo.com="" click_to_call?lang="en&amp;src=jj_signature&amp;To=%2B3" 3+%280%2=""> 9+140+61+35+13&Email=berndjagla at yahoo.com> +33 (0) 140 61 35 13 > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Upgrading to 2.9 did the trick. Don't know what the problem was, but it works... Thanks, -B -----Original Message----- From: Gregoire Pau [mailto:gregoire.pau@ebi.ac.uk] Sent: Thursday, April 23, 2009 2:02 PM To: Bernd Jagla Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] EBImage_2.6.0/R2.8.1 installation problems Hi Bernd, First, I would suggest you to switch to the latest Bioconductor release 2.4, which contains EBImage 3.0.0 (also available at http://bioconductor.org/packages/2.4/bioc/html/EBImage.html). EBImage 3.0.0 is a major release which fixes a lot of speed/bug/design issues. Reading/displaying an image is easy: > library(EBImage) > f = system.file("images","lena.gif", package="EBImage") > lena = readImage(f) > display(lena) EBImage relies on ImageMagick to read images, which itself relies on libtiff to decipher the TIFF format. Some TIFF images can contain private sections, undefined in the TIFF 6.0 specification, causing troubles to libtiff when reading (these sections are sometimes deliberately used to prevent file exchange). Please check first if you can display the images with ImageMagick 'display' command. If not, I would suggest to either update your libtiff library, or to save your images or convert them using the software provided with your microscope into a more portable lossless format (PNG, BMP, TGA...). Best regards, Greg --- Gregoire Pau EMBL Research officer http://www.ebi.ac.uk/~gpau/ Bernd Jagla wrote: > Hi, > > > > I want to use the EBImage package but when trying to access/display an image > I get the following error message. > > EBImage has never worked and this is the first time I am trying to use this > package. > > Please let me know what else I can try to make it work? > > > > > > Here is the R output: > > > > R version 2.8.1 (2008-12-22) > > Copyright (C) 2008 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > > > 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. > > > > [Previously saved workspace restored] > > > >> library(EBImage) > >> f=system.file("images","lena.gif", package="EBImage") > >> lena=readImage(f) > > Warning message: > > In .DoCall("lib_readImages", as.character(files), as.integer(colormode)) : > > requested image not found or could not be loaded > > > > additional information: > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] EBImage_2.6.0 > > > > > Gtk information: > > > > pkg-config --cflags gtk+-2.0 > > -mms-bitfields -Ic:/gtk/include/gtk-2.0 -Ic:/gtk/lib/gtk-2.0/include > -Ic:/gtk/include/atk-1.0 -Ic:/gtk/include/cairo -Ic:/gtk/include/p > > ango-1.0 -Ic:/gtk/include/glib-2.0 -Ic:/gtk/lib/glib-2.0/include > -Ic:/gtk/include/libpng12 > > > > (GTK+-bundle2.16.0-20090317_win32) > > > > ImageMagick: > > ImageMagick 6.5.1 Q16 (dll version) > > > > When trying to open some tif files I get the following error message: > > IMDisplayDoc function (DoReadImage) reported a warning. > > Imdisplay.exe: Compression algorithm does not support random access. (.) > tiff.c/TIFFErrors/324 > > Gifs, miff, PNG I can open. > > > > But eventually I am actually interested in opening TIFF files . > > > > > > Thanks for your kind help, > > > > > > Bernd > > > > > > > > > > Bernd Jagla > Bioinformatician > > Institute Pasteur > Plate-forme puces a ADN > Genopole / Institut Pasteur > 28 rue du Docteur Roux > 75724 Paris Cedex 15 > France > > > <mailto:bernd.jagla at="" pasteur.fr=""> bernd.jagla at pasteur.fr > > > tel: > > > <http: www.plaxo.com="" click_to_call?lang="en&amp;src=jj_signature&amp;To=%2B33+" %280%2=""> 9+140+61+35+13&Email=berndjagla at yahoo.com> +33 (0) 140 61 35 13 > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@herve-pages-1542
Last seen 13 hours ago
Seattle, WA, United States
Hi Bernd, Bernd Jagla wrote: [...] > >> library(EBImage) > >> f=system.file("images","lena.gif", package="EBImage") > >> lena=readImage(f) > > Warning message: > > In .DoCall("lib_readImages", as.character(files), as.integer(colormode)) : > > requested image not found or could not be loaded > lena.gif was added to EBImage in December 2008 (EBImage 2.7.9) and you are using EBImage 2.6.0 so I doubt the documentation for your version of EBImage is providing the above example. Please always install with biocLite() and make sure you are always using the current release of R + Bioconductor + EBImage (R 2.9.0 + BioC 2.4 + EBImage 3.0.0). Older versions are not supported. Cheers, H. [...] > > additional information: > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] EBImage_2.6.0 > > > > > Gtk information: > > > > pkg-config --cflags gtk+-2.0 > > -mms-bitfields -Ic:/gtk/include/gtk-2.0 -Ic:/gtk/lib/gtk-2.0/include > -Ic:/gtk/include/atk-1.0 -Ic:/gtk/include/cairo -Ic:/gtk/include/p > > ango-1.0 -Ic:/gtk/include/glib-2.0 -Ic:/gtk/lib/glib-2.0/include > -Ic:/gtk/include/libpng12 > > > > (GTK+-bundle2.16.0-20090317_win32) > > > > ImageMagick: > > ImageMagick 6.5.1 Q16 (dll version) > > > > When trying to open some tif files I get the following error message: > > IMDisplayDoc function (DoReadImage) reported a warning. > > Imdisplay.exe: Compression algorithm does not support random access. (.) > tiff.c/TIFFErrors/324 > > Gifs, miff, PNG I can open. > > > > But eventually I am actually interested in opening TIFF files . > > > > > > Thanks for your kind help, > > > > > > Bernd > > > > > > > > > > Bernd Jagla > Bioinformatician > > Institute Pasteur > Plate-forme puces a ADN > Genopole / Institut Pasteur > 28 rue du Docteur Roux > 75724 Paris Cedex 15 > France > > > <mailto:bernd.jagla at="" pasteur.fr=""> bernd.jagla at pasteur.fr > > > tel: > > > <http: www.plaxo.com="" click_to_call?lang="en&amp;src=jj_signature&amp;To=%2B3" 3+%280%2=""> 9+140+61+35+13&Email=berndjagla at yahoo.com> +33 (0) 140 61 35 13 > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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