EBImage package
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@jordi-van-gestel-5125
Last seen 6.9 years ago
Dear Mrs./Mr., I am Jordi, PhD student at the University of Groningen (the Netherlands). I am working on *Bacillus subtilis* at the Molecular Genetics lab, in which we study the expression of some genes by using fluorescent proteins. To analyze the pictures that are made during the experiments I was advised to use the EBImage package in R (I originally used MATLAB, but this was rather unstable). After reading the manual I was really impressed by the possibilities of the EBImage package. However, unfortunately, I didn't manage to install the package (I am not really a computer specialist, so I had some difficulties with following the tutorials). I performed the following steps in correspondence to the manuals that are published online: 1. First, I installed GTK+ from "http://gladewin32.sf.net" (since " http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_2. 16.0-20090317_win32.zip" and "http://www.gtk.org/download-windows.html" didn't function properly). In addition, I added to the "C:\GTK\bin" path to the system environment PATH variable. 2. Second, I installed ImageMagick from " http://www.imagemagick.org/script/binary-releases.php#windows" and placed in the following folder "C:\ImageMagick". During the installation of ImageMagick I checked the checkbox of 'Install development headers and libraries' (the 'Update executable search path' was already checked). 3. Third, I downloaded the source zip-package from " http://www.bioconductor.org/packages/release/bioc/html/EBImage.html" (I tried both 'EBImage_3.10.0.tar.gz' and 'EBImage_3.10.0.zip'). In RGui I subsequently used the botton 'Install package(s) from local zip files...' (Menu of Packages). Resulting in the following two lines in the console: > utils:::menuInstallLocal() package 'EBImage' successfully unpacked and MD5 sums checked updating HTML package descriptions After this the problems appeared: When trying to load the package (library("EBImage")): > library("EBImage") Error in library.dynam(lib, package, package.lib) : shared library 'EBImage' not found In addition: Warning message: package 'EBImage' was built under R version 2.14.0 Error: package/namespace load failed for 'EBImage' Perhaps important to know I have Windows XP Professional on my laptop. I really hope that you know the solution to this problem. Sorry, for this inconvenience. Please, let me know if you require more information. In advance, many thanks for your time. I am really appreciative for your help! Best regards, Jordi [[alternative HTML version deleted]]
Genetics EBImage Genetics EBImage • 947 views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 5 months ago
United States
On Fri, Feb 17, 2012 at 7:13 AM, Jordi van Gestel <jb.jordi at="" gmail.com=""> wrote: > Dear Mrs./Mr., > > > > I am Jordi, PhD student at the University of Groningen (the Netherlands). I > am working on *Bacillus subtilis* at the Molecular Genetics lab, in which > we study the expression of some genes by using fluorescent proteins. To > analyze the pictures that are made during the experiments I was advised to > use the EBImage package in R (I originally used MATLAB, but this was rather > unstable). > > > > After reading the manual I was really impressed by the possibilities of the > EBImage package. However, unfortunately, I didn't manage to install the > package (I am not really a computer specialist, so I had some difficulties > with following the tutorials). I performed the following steps in > correspondence to the manuals that are published online: > > > > 1. First, I installed GTK+ from ?"http://gladewin32.sf.net" (since " > http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_ 2.16.0-20090317_win32.zip" > and "http://www.gtk.org/download-windows.html" didn't function properly). > In addition, I added to the "C:\GTK\bin" path to the system environment > PATH variable. > Use the version of GTK specified in the EBImage installation vignette: http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/d oc/EBImage-installation.pdf The version specified is gtk+-2.0 2.12.9. > > > 2. Second, I installed ImageMagick from " > http://www.imagemagick.org/script/binary-releases.php#windows" and placed > in the following folder "C:\ImageMagick". During the installation of > ImageMagick I checked the checkbox of 'Install development headers and > libraries' (the 'Update executable search path' was already checked). > > > > 3. Third, I downloaded the source zip-package from " > http://www.bioconductor.org/packages/release/bioc/html/EBImage.html" (I > tried both 'EBImage_3.10.0.tar.gz' and 'EBImage_3.10.0.zip'). In RGui I > subsequently used the botton 'Install package(s) from local zip files...' > (Menu of Packages). Resulting in the following two lines in the console: > >> utils:::menuInstallLocal() > > package 'EBImage' successfully unpacked and MD5 sums checked > > updating HTML package descriptions > > > > After this the problems appeared: When trying to load the package > (library("EBImage")): > >> library("EBImage") > > Error in library.dynam(lib, package, package.lib) : > > ?shared library 'EBImage' not found > > In addition: Warning message: > > package 'EBImage' was built under R version 2.14.0 > > Error: package/namespace load failed for 'EBImage' > > Install EBImage as recommended by its page: http://bioconductor.org/packages/release/bioc/html/EBImage.html namely: source("http://bioconductor.org/biocLite.R") biocLite("EBImage") Dan > > Perhaps important to know I have Windows XP Professional on my laptop. I > really hope that you know the solution to this problem. Sorry, for this > inconvenience. Please, let me know if you require more information. In > advance, many thanks for your time. I am really appreciative for your help! > > > > Best regards, > > > > Jordi > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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
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Dear Dan, Thank you for your reply! I installed the EBImage package as you recommended. But I still get one error message. Namely, when I load the package (library("EBImage")), I get the following complain: Error in inDL(x, as.logical(local), as.logical(now), ...) : cannot initialize ImageMagick Error: package/namespace load failed for 'EBImage' I hope you know what is going wrong. Sorry for the inconvenience and again thank you very much for your help! Jordi On Sat, Feb 18, 2012 at 5:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Fri, Feb 17, 2012 at 7:13 AM, Jordi van Gestel <jb.jordi@gmail.com> > wrote: > > Dear Mrs./Mr., > > > > > > > > I am Jordi, PhD student at the University of Groningen (the > Netherlands). I > > am working on *Bacillus subtilis* at the Molecular Genetics lab, in which > > we study the expression of some genes by using fluorescent proteins. To > > analyze the pictures that are made during the experiments I was advised > to > > use the EBImage package in R (I originally used MATLAB, but this was > rather > > unstable). > > > > > > > > After reading the manual I was really impressed by the possibilities of > the > > EBImage package. However, unfortunately, I didn't manage to install the > > package (I am not really a computer specialist, so I had some > difficulties > > with following the tutorials). I performed the following steps in > > correspondence to the manuals that are published online: > > > > > > > > 1. First, I installed GTK+ from "http://gladewin32.sf.net" (since " > > > http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_ 2.16.0-20090317_win32.zip > " > > and "http://www.gtk.org/download-windows.html" didn't function > properly). > > In addition, I added to the "C:\GTK\bin" path to the system environment > > PATH variable. > > > > Use the version of GTK specified in the EBImage installation vignette: > > http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst /doc/EBImage-installation.pdf > > The version specified is gtk+-2.0 2.12.9. > > > > > > > > 2. Second, I installed ImageMagick from " > > http://www.imagemagick.org/script/binary-releases.php#windows" and > placed > > in the following folder "C:\ImageMagick". During the installation of > > ImageMagick I checked the checkbox of 'Install development headers and > > libraries' (the 'Update executable search path' was already checked). > > > > > > > > 3. Third, I downloaded the source zip-package from " > > http://www.bioconductor.org/packages/release/bioc/html/EBImage.html" (I > > tried both 'EBImage_3.10.0.tar.gz' and 'EBImage_3.10.0.zip'). In RGui I > > subsequently used the botton 'Install package(s) from local zip files...' > > (Menu of Packages). Resulting in the following two lines in the console: > > > >> utils:::menuInstallLocal() > > > > package 'EBImage' successfully unpacked and MD5 sums checked > > > > updating HTML package descriptions > > > > > > > > After this the problems appeared: When trying to load the package > > (library("EBImage")): > > > >> library("EBImage") > > > > Error in library.dynam(lib, package, package.lib) : > > > > shared library 'EBImage' not found > > > > In addition: Warning message: > > > > package 'EBImage' was built under R version 2.14.0 > > > > Error: package/namespace load failed for 'EBImage' > > > > > > > Install EBImage as recommended by its page: > http://bioconductor.org/packages/release/bioc/html/EBImage.html > > namely: > source("http://bioconductor.org/biocLite.R") > biocLite("EBImage") > > Dan > > > > > Perhaps important to know I have Windows XP Professional on my laptop. I > > really hope that you know the solution to this problem. Sorry, for this > > inconvenience. Please, let me know if you require more information. In > > advance, many thanks for your time. I am really appreciative for your > help! > > > > > > > > Best regards, > > > > > > > > Jordi > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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]]
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On Thu, Feb 23, 2012 at 2:58 PM, Jordi van Gestel <jb.jordi at="" gmail.com=""> wrote: > Dear Dan, > > Thank you for your reply! I installed the EBImage package as you > recommended. But I still get one error message. Namely, when I load the > package (library("EBImage")), I get the following complain: > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > ? cannot initialize ImageMagick > Error: package/namespace load failed for 'EBImage' > > I hope you know what is going wrong. Sorry for the inconvenience and again > thank you very much for your help! > You don't specify which version of R you are running, but it looks like it's lower than 2.14 which is the current release version. Please update to R-2.14. Make sure ImageMagick is installed and that its directory has indeed been added to the PATH. If you still have problems, please include the output of sessionInfo() in your reply. Thanks, Dan > Jordi > > > On Sat, Feb 18, 2012 at 5:45 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Fri, Feb 17, 2012 at 7:13 AM, Jordi van Gestel <jb.jordi at="" gmail.com=""> >> wrote: >> > Dear Mrs./Mr., >> > >> > >> > >> > I am Jordi, PhD student at the University of Groningen (the >> > Netherlands). I >> > am working on *Bacillus subtilis* at the Molecular Genetics lab, in >> > which >> > we study the expression of some genes by using fluorescent proteins. To >> > analyze the pictures that are made during the experiments I was advised >> > to >> > use the EBImage package in R (I originally used MATLAB, but this was >> > rather >> > unstable). >> > >> > >> > >> > After reading the manual I was really impressed by the possibilities of >> > the >> > EBImage package. However, unfortunately, I didn't manage to install the >> > package (I am not really a computer specialist, so I had some >> > difficulties >> > with following the tutorials). I performed the following steps in >> > correspondence to the manuals that are published online: >> > >> > >> > >> > 1. First, I installed GTK+ from ?"http://gladewin32.sf.net" (since " >> > >> > http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bund le_2.16.0-20090317_win32.zip" >> > and "http://www.gtk.org/download-windows.html" didn't function >> > properly). >> > In addition, I added to the "C:\GTK\bin" path to the system environment >> > PATH variable. >> > >> >> Use the version of GTK ?specified in the EBImage installation vignette: >> >> http://bioconductor.org/packages/release/bioc/vignettes/EBImage/ins t/doc/EBImage-installation.pdf >> >> The version specified is gtk+-2.0 2.12.9. >> >> >> > >> > >> > 2. Second, I installed ImageMagick from " >> > http://www.imagemagick.org/script/binary-releases.php#windows" and >> > placed >> > in the following folder "C:\ImageMagick". During the installation of >> > ImageMagick I checked the checkbox of 'Install development headers and >> > libraries' (the 'Update executable search path' was already checked). >> > >> > >> > >> > 3. Third, I downloaded the source zip-package from " >> > http://www.bioconductor.org/packages/release/bioc/html/EBImage.html" (I >> > tried both 'EBImage_3.10.0.tar.gz' and 'EBImage_3.10.0.zip'). In RGui I >> > subsequently used the botton 'Install package(s) from local zip >> > files...' >> > (Menu of Packages). Resulting in the following two lines in the console: >> > >> >> utils:::menuInstallLocal() >> > >> > package 'EBImage' successfully unpacked and MD5 sums checked >> > >> > updating HTML package descriptions >> > >> > >> > >> > After this the problems appeared: When trying to load the package >> > (library("EBImage")): >> > >> >> library("EBImage") >> > >> > Error in library.dynam(lib, package, package.lib) : >> > >> > ?shared library 'EBImage' not found >> > >> > In addition: Warning message: >> > >> > package 'EBImage' was built under R version 2.14.0 >> > >> > Error: package/namespace load failed for 'EBImage' >> > >> > >> >> >> Install EBImage as recommended by its page: >> http://bioconductor.org/packages/release/bioc/html/EBImage.html >> >> namely: >> source("http://bioconductor.org/biocLite.R") >> biocLite("EBImage") >> >> Dan >> >> > >> > Perhaps important to know I have Windows XP Professional on my laptop. I >> > really hope that you know the solution to this problem. Sorry, for this >> > inconvenience. Please, let me know if you require more information. In >> > advance, many thanks for your time. I am really appreciative for your >> > help! >> > >> > >> > >> > Best regards, >> > >> > >> > >> > Jordi >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 > >
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