unable to readImage using EBImage package
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Hi, I'm Diyanah. Currently I've been working on my final year project (Offline Signature Verification System). I'm required to use R programming and I've found that EBImage going well with R in image processing. I've successfully install R and EBImage package (along with ImageMagick and GTK). The thing is, when I try the command that I get from the "Introduction to EBImage" manual, I receive error/warning message. I hope you may help me solving these problem. I have already change the directory to where the image is placed, and I have confirmed it by calling a .txt file and it is a success, but when I try for the image, I received these: -- output of sessionInfo(): > f =system.file("Images","user186g1.tif", pakage="EBImage") > user186g1 = readImage (f) Warning message: In readImage(f) : requested image not found or could not be loaded I try calling the directory by the using the PATH (I'm not sure whether the command is correct): > f =system.file("D:\\FYP ~\\image","user186g1.tif", pakage="EBImage") > user186g1 = readImage(f) Warning message: In readImage(f) : requested image not found or could not be loaded -- Sent via the guest posting facility at bioconductor.org.
EBImage EBImage • 3.1k views
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Dan Tenenbaum ★ 8.2k
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On Mar 2, 2012 11:25 PM, "diyanah [guest]" <guest@bioconductor.org> wrote: > > > Hi, I'm Diyanah. > Currently I've been working on my final year project (Offline Signature Verification System). I'm required to use R programming and I've found that EBImage going well with R in image processing. I've successfully install R and EBImage package (along with ImageMagick and GTK). The thing is, when I try the command that I get from the "Introduction to EBImage" manual, I receive error/warning message. I hope you may help me solving these problem. > > > I have already change the directory to where the image is placed, and I have confirmed it by calling a .txt file and it is a success, but when I try for the image, I received these: > > -- output of sessionInfo(): > > > f =system.file("Images","user186g1.tif", pakage="EBImage") You spelled 'package' wrong. > > user186g1 = readImage (f) > Warning message: > In readImage(f) : requested image not found or could not be loaded > > > I try calling the directory by the using the PATH (I'm not sure whether the command is correct): > > > > f =system.file("D:\\FYP ~\\image","user186g1.tif", pakage="EBImage") Misspelled 'package' again. Dan > > user186g1 = readImage(f) > Warning message: > In readImage(f) : requested image not found or could not be loaded > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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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Dan Tenenbaum ★ 8.2k
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Please CC the bioconductor list. Also, please read the posting guide, and provide the output of the sessionInfo() function. See below. On Sat, Mar 3, 2012 at 1:04 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > I've correct the spelling, but I still receive the same warning message. Can > you help me. > > > On Sat, Mar 3, 2012 at 3:58 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> >> On Mar 2, 2012 11:25 PM, "diyanah [guest]" <guest at="" bioconductor.org=""> wrote: >> > >> > >> > Hi, I'm Diyanah. >> > Currently I've been working on my final year project (Offline Signature >> > Verification System). I'm required to use R programming and I've found that >> > EBImage going well with R in image processing. I've successfully install R >> > and EBImage package (along with ImageMagick and GTK). The thing is, when I >> > try the command that I get from the "Introduction to EBImage" manual, I >> > receive error/warning message. I hope you may help me solving these problem. >> > >> > >> > I have already change the directory to where the image is placed, and I >> > have confirmed it by calling a .txt file and it is a success, but when I try >> > for the image, I received these: >> > >> > ?-- output of sessionInfo(): >> > >> > > f =system.file("Images","user186g1.tif", pakage="EBImage") >> >> You spelled 'package' wrong. I'm not sure what version of R or EBImage you are using, but in the current release version of EBImage, there is no file "user186g1.tif" anywhere in the package. What the above command does is look inside the installed package for a file. Perhaps you want to manipulate a file you have created? If so, you don't want to use system.file() but instead point to the directory where you created the file. Sounds like you are already in the right directory, so what happens if you just do this: f =system.file("user186g1.tif") user186g1 = readImage (f) ? >> >> > > user186g1 = readImage (f) >> > Warning message: >> > In readImage(f) : requested image not found or could not be loaded >> > >> > >> > I try calling the directory by the using the PATH (I'm not sure whether >> > the command is correct): >> > >> > >> > > f =system.file("D:\\FYP ~\\image","user186g1.tif", pakage="EBImage") >> This is now how you set or get the PATH environment variable. In any case that is not what you want to do, I think; use getwd() to find out what directory you are in. and setwd() to change directories. Dan >> Misspelled 'package' again. >> Dan >> >> > > user186g1 = readImage(f) >> > Warning message: >> > In readImage(f) : requested image not found or could not be loaded >> > >> > -- >> > 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 > > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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On Sat, Mar 3, 2012 at 2:42 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > Please CC the bioconductor list. Also, please read the posting guide, > and provide the output of the sessionInfo() function. > > See below. > > On Sat, Mar 3, 2012 at 1:04 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: >> I've correct the spelling, but I still receive the same warning message. Can >> you help me. >> >> >> On Sat, Mar 3, 2012 at 3:58 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >>> >>> >>> On Mar 2, 2012 11:25 PM, "diyanah [guest]" <guest at="" bioconductor.org=""> wrote: >>> > >>> > >>> > Hi, I'm Diyanah. >>> > Currently I've been working on my final year project (Offline Signature >>> > Verification System). I'm required to use R programming and I've found that >>> > EBImage going well with R in image processing. I've successfully install R >>> > and EBImage package (along with ImageMagick and GTK). The thing is, when I >>> > try the command that I get from the "Introduction to EBImage" manual, I >>> > receive error/warning message. I hope you may help me solving these problem. >>> > >>> > >>> > I have already change the directory to where the image is placed, and I >>> > have confirmed it by calling a .txt file and it is a success, but when I try >>> > for the image, I received these: >>> > >>> > ?-- output of sessionInfo(): >>> > >>> > > f =system.file("Images","user186g1.tif", pakage="EBImage") >>> >>> You spelled 'package' wrong. > > I'm not sure what version of R or EBImage you are using, but in the > current release version of EBImage, there is no file "user186g1.tif" > anywhere in the package. What the above command does is look inside > the installed package for a file. Perhaps you want to manipulate a > file you have created? If so, you don't want to use system.file() but > instead point to the directory where you created the file. > Sounds like you are already in the right directory, so what happens if > you just do this: > > ?f =system.file("user186g1.tif") > user186g1 = readImage (f) > Sorry, typo, I meant to say: user186g1 = readImage("user186g1.tif") Dan > ? > >>> >>> > > user186g1 = readImage (f) >>> > Warning message: >>> > In readImage(f) : requested image not found or could not be loaded >>> > >>> > >>> > I try calling the directory by the using the PATH (I'm not sure whether >>> > the command is correct): >>> > >>> > >>> > > f =system.file("D:\\FYP ~\\image","user186g1.tif", pakage="EBImage") >>> > > This is now how you set or get the PATH environment variable. In any > case that is not what you want to do, I think; use > > getwd() > to find out what directory you are in. > and > setwd() > to change directories. > > Dan > > >>> Misspelled 'package' again. >>> Dan >>> >>> > > user186g1 = readImage(f) >>> > Warning message: >>> > In readImage(f) : requested image not found or could not be loaded >>> > >>> > -- >>> > 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 >> >> >> >> >> -- >> Nurdiyanah Bt Hj Jambari >> Student >> Faculty of Engineering >> Bachelor Engineering of Computer & Communication System Engineering >> University Putra Malaysia
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Hi, Please help me with these problem. Every time I'm trying to display the example image, I receive these kind of pop-up warning: ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: 'C:\Windows\system32\etc\pango\pango.modules' You may be able to recreate this file by running pango-querymodules. (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line 1561 (g_object_ ref): assertion `G_IS_OBJECT (object)' failed ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 (_pango_engine_sh ape_shape): assertion `PANGO_IS_FONT (font)' failed I have try several method that I found searching from the internet, but still I could not fix these problem. Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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Dan Tenenbaum ★ 8.2k
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On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > Hi, > > Please help me with these problem. Every time I'm trying to display the > example image, I receive these kind of pop-up warning: > > > ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded modules > were found. Pango will not work correctly. This probably means > there was an error in the creation of: > ? 'C:\Windows\system32\etc\pango\pango.modules' > You may be able to recreate this file by running pango-querymodules. > > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line 1561 > (g_object_ > ref): assertion `G_IS_OBJECT (object)' failed > > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 > (_pango_engine_sh > ape_shape): assertion `PANGO_IS_FONT (font)' failed > > > I have try several method that I found searching from the internet, but > still I could not fix these problem. It's difficult for us to help without knowing the exact commands you tried that caused this error, and more information about your system (e.g., the output of the sessionInfo() function). Dan > > > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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This error happen while I'm trying to view the example image. These is because I read from the manual, if I want to make sure that the package is install correctly, it should be able to display the "lena.gif" image: >library("EBImage") >f = system.file("images", "lena.gif", package="EBImage") >lena = readImage(f) >display(lena) On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari <yanadj28@gmail.com> > wrote: > > Hi, > > > > Please help me with these problem. Every time I'm trying to display the > > example image, I receive these kind of pop-up warning: > > > > > > ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded modules > > were found. Pango will not work correctly. This probably means > > there was an error in the creation of: > > 'C:\Windows\system32\etc\pango\pango.modules' > > You may be able to recreate this file by running pango- querymodules. > > > > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line 1561 > > (g_object_ > > ref): assertion `G_IS_OBJECT (object)' failed > > > > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 > > (_pango_engine_sh > > ape_shape): assertion `PANGO_IS_FONT (font)' failed > > > > > > I have try several method that I found searching from the internet, but > > still I could not fix these problem. > > It's difficult for us to help without knowing the exact commands you > tried that caused this error, and more information about your system > (e.g., the output of the sessionInfo() function). > > Dan > > > > > > > > Nurdiyanah Bt Hj Jambari > > Student > > Faculty of Engineering > > Bachelor Engineering of Computer & Communication System Engineering > > University Putra Malaysia > -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > This error happen while I'm trying to view the example image. These is > because I read from the manual, if I want to make sure that the package is > install correctly, it should be able to display the "lena.gif" image: > > >>library("EBImage") >>f = system.file("images", "lena.gif", package="EBImage") >>lena = readImage(f) >>display(lena) > > > Please post the output of sessionInfo() Thanks Dan > > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> wrote: >> > Hi, >> > >> > Please help me with these problem. Every time I'm trying to display the >> > example image, I receive these kind of pop-up warning: >> > >> > >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded >> > modules >> > were found. Pango will not work correctly. This probably means >> > there was an error in the creation of: >> > ? 'C:\Windows\system32\etc\pango\pango.modules' >> > You may be able to recreate this file by running pango- querymodules. >> > >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line 1561 >> > (g_object_ >> > ref): assertion `G_IS_OBJECT (object)' failed >> > >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 >> > (_pango_engine_sh >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed >> > >> > >> > I have try several method that I found searching from the internet, but >> > still I could not fix these problem. >> >> It's difficult for us to help without knowing the exact commands you >> tried that caused this error, and more information about your system >> (e.g., the output of the sessionInfo() function). >> >> Dan >> >> >> > >> > >> > Nurdiyanah Bt Hj Jambari >> > Student >> > Faculty of Engineering >> > Bachelor Engineering of Computer & Communication System Engineering >> > University Putra Malaysia > > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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Dan Tenenbaum ★ 8.2k
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On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > Sorry, I forgot to mention that the system will go to not responding and > need to be closed after the pop-up message appear. > Please post the output of sessionInfo(), run it immediately before the command that causes the error. Thanks, Dan > > > > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> wrote: >> > This error happen while I'm trying to view the example image. These is >> > because I read from the manual, if I want to make sure that the package >> > is >> > install correctly, it should be able to display the "lena.gif" image: >> > >> > >> >>library("EBImage") >> >>f = system.file("images", "lena.gif", package="EBImage") >> >>lena = readImage(f) >> >>display(lena) >> > >> > >> > >> Please post the output of >> sessionInfo() >> Thanks >> Dan >> >> >> > >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari >> >> <yanadj28 at="" gmail.com=""> >> >> wrote: >> >> > Hi, >> >> > >> >> > Please help me with these problem. Every time I'm trying to display >> >> > the >> >> > example image, I receive these kind of pop-up warning: >> >> > >> >> > >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded >> >> > modules >> >> > were found. Pango will not work correctly. This probably means >> >> > there was an error in the creation of: >> >> > ? 'C:\Windows\system32\etc\pango\pango.modules' >> >> > You may be able to recreate this file by running pango- querymodules. >> >> > >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line 1561 >> >> > (g_object_ >> >> > ref): assertion `G_IS_OBJECT (object)' failed >> >> > >> >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 >> >> > (_pango_engine_sh >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed >> >> > >> >> > >> >> > I have try several method that I found searching from the internet, >> >> > but >> >> > still I could not fix these problem. >> >> >> >> It's difficult for us to help without knowing the exact commands you >> >> tried that caused this error, and more information about your system >> >> (e.g., the output of the sessionInfo() function). >> >> >> >> Dan >> >> >> >> >> >> > >> >> > >> >> > Nurdiyanah Bt Hj Jambari >> >> > Student >> >> > Faculty of Engineering >> >> > Bachelor Engineering of Computer & Communication System Engineering >> >> > University Putra Malaysia >> > >> > >> > >> > >> > -- >> > Nurdiyanah Bt Hj Jambari >> > Student >> > Faculty of Engineering >> > Bachelor Engineering of Computer & Communication System Engineering >> > University Putra Malaysia > > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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Sorry, I miss understood your request. This is the output of my sessionInfo(): > sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari <yanadj28@gmail.com> > wrote: > > Sorry, I forgot to mention that the system will go to not responding and > > need to be closed after the pop-up message appear. > > > > Please post the output of sessionInfo(), run it immediately before the > command that causes the error. > > Thanks, > Dan > > > > > > > > > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > >> > >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari <yanadj28@gmail.com> > >> wrote: > >> > This error happen while I'm trying to view the example image. These is > >> > because I read from the manual, if I want to make sure that the > package > >> > is > >> > install correctly, it should be able to display the "lena.gif" image: > >> > > >> > > >> >>library("EBImage") > >> >>f = system.file("images", "lena.gif", package="EBImage") > >> >>lena = readImage(f) > >> >>display(lena) > >> > > >> > > >> > > >> Please post the output of > >> sessionInfo() > >> Thanks > >> Dan > >> > >> > >> > > >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> > wrote: > >> >> > >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari > >> >> <yanadj28@gmail.com> > >> >> wrote: > >> >> > Hi, > >> >> > > >> >> > Please help me with these problem. Every time I'm trying to display > >> >> > the > >> >> > example image, I receive these kind of pop-up warning: > >> >> > > >> >> > > >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded > >> >> > modules > >> >> > were found. Pango will not work correctly. This probably means > >> >> > there was an error in the creation of: > >> >> > 'C:\Windows\system32\etc\pango\pango.modules' > >> >> > You may be able to recreate this file by running > pango-querymodules. > >> >> > > >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line > 1561 > >> >> > (g_object_ > >> >> > ref): assertion `G_IS_OBJECT (object)' failed > >> >> > > >> >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 > >> >> > (_pango_engine_sh > >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed > >> >> > > >> >> > > >> >> > I have try several method that I found searching from the internet, > >> >> > but > >> >> > still I could not fix these problem. > >> >> > >> >> It's difficult for us to help without knowing the exact commands you > >> >> tried that caused this error, and more information about your system > >> >> (e.g., the output of the sessionInfo() function). > >> >> > >> >> Dan > >> >> > >> >> > >> >> > > >> >> > > >> >> > Nurdiyanah Bt Hj Jambari > >> >> > Student > >> >> > Faculty of Engineering > >> >> > Bachelor Engineering of Computer & Communication System Engineering > >> >> > University Putra Malaysia > >> > > >> > > >> > > >> > > >> > -- > >> > Nurdiyanah Bt Hj Jambari > >> > Student > >> > Faculty of Engineering > >> > Bachelor Engineering of Computer & Communication System Engineering > >> > University Putra Malaysia > > > > > > > > > > -- > > Nurdiyanah Bt Hj Jambari > > Student > > Faculty of Engineering > > Bachelor Engineering of Computer & Communication System Engineering > > University Putra Malaysia > -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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They're also interested in details about EBImage, so: > library("EBImage"); > sessionInfo(); Over and out. /Henrik On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > Sorry, I miss understood your request. This is the output of my > sessionInfo(): > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United > States.1252 ? ?LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > > > On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > >> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> wrote: >> > Sorry, I forgot to mention that the system will go to not responding and >> > need to be closed after the pop-up message appear. >> > >> >> Please post the output of sessionInfo(), run it immediately before the >> command that causes the error. >> >> Thanks, >> Dan >> >> > >> > >> > >> > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> wrote: >> >> >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> >> wrote: >> >> > This error happen while I'm trying to view the example image. These is >> >> > because I read from the manual, if I want to make sure that the >> package >> >> > is >> >> > install correctly, it should be able to display the "lena.gif" image: >> >> > >> >> > >> >> >>library("EBImage") >> >> >>f = system.file("images", "lena.gif", package="EBImage") >> >> >>lena = readImage(f) >> >> >>display(lena) >> >> > >> >> > >> >> > >> >> Please post the output of >> >> sessionInfo() >> >> Thanks >> >> Dan >> >> >> >> >> >> > >> >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> > wrote: >> >> >> >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari >> >> >> <yanadj28 at="" gmail.com=""> >> >> >> wrote: >> >> >> > Hi, >> >> >> > >> >> >> > Please help me with these problem. Every time I'm trying to display >> >> >> > the >> >> >> > example image, I receive these kind of pop-up warning: >> >> >> > >> >> >> > >> >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically loaded >> >> >> > modules >> >> >> > were found. Pango will not work correctly. This probably means >> >> >> > there was an error in the creation of: >> >> >> > ? 'C:\Windows\system32\etc\pango\pango.modules' >> >> >> > You may be able to recreate this file by running >> pango-querymodules. >> >> >> > >> >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line >> 1561 >> >> >> > (g_object_ >> >> >> > ref): assertion `G_IS_OBJECT (object)' failed >> >> >> > >> >> >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 >> >> >> > (_pango_engine_sh >> >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed >> >> >> > >> >> >> > >> >> >> > I have try several method that I found searching from the internet, >> >> >> > but >> >> >> > still I could not fix these problem. >> >> >> >> >> >> It's difficult for us to help without knowing the exact commands you >> >> >> tried that caused this error, and more information about your system >> >> >> (e.g., the output of the sessionInfo() function). >> >> >> >> >> >> Dan >> >> >> >> >> >> >> >> >> > >> >> >> > >> >> >> > Nurdiyanah Bt Hj Jambari >> >> >> > Student >> >> >> > Faculty of Engineering >> >> >> > Bachelor Engineering of Computer & Communication System Engineering >> >> >> > University Putra Malaysia >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Nurdiyanah Bt Hj Jambari >> >> > Student >> >> > Faculty of Engineering >> >> > Bachelor Engineering of Computer & Communication System Engineering >> >> > University Putra Malaysia >> > >> > >> > >> > >> > -- >> > Nurdiyanah Bt Hj Jambari >> > Student >> > Faculty of Engineering >> > Bachelor Engineering of Computer & Communication System Engineering >> > University Putra Malaysia >> > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia > > ? ? ? ?[[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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@nurdiyanah-jambari-4934
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---------- Forwarded message ---------- From: Nurdiyanah Jambari <yanadj28@gmail.com> Date: Wed, Mar 7, 2012 at 10:50 AM Subject: Re: [BioC] unable to readImage using EBImage package To: Henrik Bengtsson <hb@biostat.ucsf.edu> > library("EBImage") > sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] EBImage_3.10.0 abind_1.4-0 loaded via a namespace (and not attached): [1] tools_2.14.1 On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson <hb@biostat.ucsf.edu>wrote: > They're also interested in details about EBImage, so: > > > library("EBImage"); > > sessionInfo(); > > Over and out. > > /Henrik > > On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari <yanadj28@gmail.com> > wrote: > > Sorry, I miss understood your request. This is the output of my > > sessionInfo(): > > > >> sessionInfo() > > R version 2.14.1 (2011-12-22) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > States.1252 LC_MONETARY=English_United States.1252 > > LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > > > > > On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > > > >> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari <yanadj28@gmail.com> > >> wrote: > >> > Sorry, I forgot to mention that the system will go to not responding > and > >> > need to be closed after the pop-up message appear. > >> > > >> > >> Please post the output of sessionInfo(), run it immediately before the > >> command that causes the error. > >> > >> Thanks, > >> Dan > >> > >> > > >> > > >> > > >> > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> wrote: > >> >> > >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari < > yanadj28@gmail.com> > >> >> wrote: > >> >> > This error happen while I'm trying to view the example image. > These is > >> >> > because I read from the manual, if I want to make sure that the > >> package > >> >> > is > >> >> > install correctly, it should be able to display the "lena.gif" > image: > >> >> > > >> >> > > >> >> >>library("EBImage") > >> >> >>f = system.file("images", "lena.gif", package="EBImage") > >> >> >>lena = readImage(f) > >> >> >>display(lena) > >> >> > > >> >> > > >> >> > > >> >> Please post the output of > >> >> sessionInfo() > >> >> Thanks > >> >> Dan > >> >> > >> >> > >> >> > > >> >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> >> > wrote: > >> >> >> > >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari > >> >> >> <yanadj28@gmail.com> > >> >> >> wrote: > >> >> >> > Hi, > >> >> >> > > >> >> >> > Please help me with these problem. Every time I'm trying to > display > >> >> >> > the > >> >> >> > example image, I receive these kind of pop-up warning: > >> >> >> > > >> >> >> > > >> >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically > loaded > >> >> >> > modules > >> >> >> > were found. Pango will not work correctly. This probably means > >> >> >> > there was an error in the creation of: > >> >> >> > 'C:\Windows\system32\etc\pango\pango.modules' > >> >> >> > You may be able to recreate this file by running > >> pango-querymodules. > >> >> >> > > >> >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: line > >> 1561 > >> >> >> > (g_object_ > >> >> >> > ref): assertion `G_IS_OBJECT (object)' failed > >> >> >> > > >> >> >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 > >> >> >> > (_pango_engine_sh > >> >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed > >> >> >> > > >> >> >> > > >> >> >> > I have try several method that I found searching from the > internet, > >> >> >> > but > >> >> >> > still I could not fix these problem. > >> >> >> > >> >> >> It's difficult for us to help without knowing the exact commands > you > >> >> >> tried that caused this error, and more information about your > system > >> >> >> (e.g., the output of the sessionInfo() function). > >> >> >> > >> >> >> Dan > >> >> >> > >> >> >> > >> >> >> > > >> >> >> > > >> >> >> > Nurdiyanah Bt Hj Jambari > >> >> >> > Student > >> >> >> > Faculty of Engineering > >> >> >> > Bachelor Engineering of Computer & Communication System > Engineering > >> >> >> > University Putra Malaysia > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Nurdiyanah Bt Hj Jambari > >> >> > Student > >> >> > Faculty of Engineering > >> >> > Bachelor Engineering of Computer & Communication System Engineering > >> >> > University Putra Malaysia > >> > > >> > > >> > > >> > > >> > -- > >> > Nurdiyanah Bt Hj Jambari > >> > Student > >> > Faculty of Engineering > >> > Bachelor Engineering of Computer & Communication System Engineering > >> > University Putra Malaysia > >> > > > > > > > > -- > > Nurdiyanah Bt Hj Jambari > > Student > > Faculty of Engineering > > Bachelor Engineering of Computer & Communication System Engineering > > University Putra Malaysia > > > > [[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 > -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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On Tue, Mar 6, 2012 at 7:25 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > > > ---------- Forwarded message ---------- > From: Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> > Date: Wed, Mar 7, 2012 at 10:50 AM > Subject: Re: [BioC] unable to readImage using EBImage package > To: Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> > > >> library("EBImage") > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United > States.1252??? LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > other attached packages: > [1] EBImage_3.10.0 abind_1.4-0 > > loaded via a namespace (and not attached): > [1] tools_2.14.1 > > > > I have found that for Windows, EBImage does not like the most recent version of GTK+. You should install the version specified in the EBImage installation vignette: http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_2. 16.6-20100912_win32.zip Dan > > > On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> > wrote: >> >> They're also interested in details about EBImage, so: >> >> > library("EBImage"); >> > sessionInfo(); >> >> Over and out. >> >> /Henrik >> >> On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> wrote: >> > Sorry, I miss understood your request. This is the output of my >> > sessionInfo(): >> > >> >> sessionInfo() >> > R version 2.14.1 (2011-12-22) >> > Platform: i386-pc-mingw32/i386 (32-bit) >> > >> > locale: >> > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United >> > States.1252 ? ?LC_MONETARY=English_United States.1252 >> > LC_NUMERIC=C >> > [5] LC_TIME=English_United States.1252 >> > >> > attached base packages: >> > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> > >> > >> > >> > On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> > >> >> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> >> wrote: >> >> > Sorry, I forgot to mention that the system will go to not responding >> >> > and >> >> > need to be closed after the pop-up message appear. >> >> > >> >> >> >> Please post the output of sessionInfo(), run it immediately before the >> >> command that causes the error. >> >> >> >> Thanks, >> >> Dan >> >> >> >> > >> >> > >> >> > >> >> > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> wrote: >> >> >> >> >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari >> >> >> <yanadj28 at="" gmail.com=""> >> >> >> wrote: >> >> >> > This error happen while I'm trying to view the example image. >> >> >> > These is >> >> >> > because I read from the manual, if I want to make sure that the >> >> package >> >> >> > is >> >> >> > install correctly, it should be able to display the "lena.gif" >> >> >> > image: >> >> >> > >> >> >> > >> >> >> >>library("EBImage") >> >> >> >>f = system.file("images", "lena.gif", package="EBImage") >> >> >> >>lena = readImage(f) >> >> >> >>display(lena) >> >> >> > >> >> >> > >> >> >> > >> >> >> Please post the output of >> >> >> sessionInfo() >> >> >> Thanks >> >> >> Dan >> >> >> >> >> >> >> >> >> > >> >> >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> >> > wrote: >> >> >> >> >> >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari >> >> >> >> <yanadj28 at="" gmail.com=""> >> >> >> >> wrote: >> >> >> >> > Hi, >> >> >> >> > >> >> >> >> > Please help me with these problem. Every time I'm trying to >> >> >> >> > display >> >> >> >> > the >> >> >> >> > example image, I receive these kind of pop-up warning: >> >> >> >> > >> >> >> >> > >> >> >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically >> >> >> >> > loaded >> >> >> >> > modules >> >> >> >> > were found. Pango will not work correctly. This probably means >> >> >> >> > there was an error in the creation of: >> >> >> >> > ? 'C:\Windows\system32\etc\pango\pango.modules' >> >> >> >> > You may be able to recreate this file by running >> >> pango-querymodules. >> >> >> >> > >> >> >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: >> >> >> >> > line >> >> 1561 >> >> >> >> > (g_object_ >> >> >> >> > ref): assertion `G_IS_OBJECT (object)' failed >> >> >> >> > >> >> >> >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line 68 >> >> >> >> > (_pango_engine_sh >> >> >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed >> >> >> >> > >> >> >> >> > >> >> >> >> > I have try several method that I found searching from the >> >> >> >> > internet, >> >> >> >> > but >> >> >> >> > still I could not fix these problem. >> >> >> >> >> >> >> >> It's difficult for us to help without knowing the exact commands >> >> >> >> you >> >> >> >> tried that caused this error, and more information about your >> >> >> >> system >> >> >> >> (e.g., the output of the sessionInfo() function). >> >> >> >> >> >> >> >> Dan >> >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> > >> >> >> >> > Nurdiyanah Bt Hj Jambari >> >> >> >> > Student >> >> >> >> > Faculty of Engineering >> >> >> >> > Bachelor Engineering of Computer & Communication System >> >> >> >> > Engineering >> >> >> >> > University Putra Malaysia >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > Nurdiyanah Bt Hj Jambari >> >> >> > Student >> >> >> > Faculty of Engineering >> >> >> > Bachelor Engineering of Computer & Communication System >> >> >> > Engineering >> >> >> > University Putra Malaysia >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Nurdiyanah Bt Hj Jambari >> >> > Student >> >> > Faculty of Engineering >> >> > Bachelor Engineering of Computer & Communication System Engineering >> >> > University Putra Malaysia >> >> >> > >> > >> > >> > -- >> > Nurdiyanah Bt Hj Jambari >> > Student >> > Faculty of Engineering >> > Bachelor Engineering of Computer & Communication System Engineering >> > University Putra Malaysia >> > >> > ? ? ? ?[[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 > > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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Can you please help me explain on how to place/install this GTK file. I hope I didn't wrongly place it. I've been searching in the internet, but there is no specific step for it. thank you. On Wed, Mar 7, 2012 at 12:11 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Tue, Mar 6, 2012 at 7:25 PM, Nurdiyanah Jambari <yanadj28@gmail.com> > wrote: > > > > > > ---------- Forwarded message ---------- > > From: Nurdiyanah Jambari <yanadj28@gmail.com> > > Date: Wed, Mar 7, 2012 at 10:50 AM > > Subject: Re: [BioC] unable to readImage using EBImage package > > To: Henrik Bengtsson <hb@biostat.ucsf.edu> > > > > > >> library("EBImage") > > > >> sessionInfo() > > R version 2.14.1 (2011-12-22) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > States.1252 LC_MONETARY=English_United States.1252 > > LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] EBImage_3.10.0 abind_1.4-0 > > > > loaded via a namespace (and not attached): > > [1] tools_2.14.1 > > > > > > > > > > I have found that for Windows, EBImage does not like the most recent > version of GTK+. > You should install the version specified in the EBImage installation > vignette: > > > http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_ 2.16.6-20100912_win32.zip > > Dan > > > > > > > > On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson <hb@biostat.ucsf.edu> > > wrote: > >> > >> They're also interested in details about EBImage, so: > >> > >> > library("EBImage"); > >> > sessionInfo(); > >> > >> Over and out. > >> > >> /Henrik > >> > >> On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari <yanadj28@gmail.com> > >> wrote: > >> > Sorry, I miss understood your request. This is the output of my > >> > sessionInfo(): > >> > > >> >> sessionInfo() > >> > R version 2.14.1 (2011-12-22) > >> > Platform: i386-pc-mingw32/i386 (32-bit) > >> > > >> > locale: > >> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > >> > States.1252 LC_MONETARY=English_United States.1252 > >> > LC_NUMERIC=C > >> > [5] LC_TIME=English_United States.1252 > >> > > >> > attached base packages: > >> > [1] stats graphics grDevices utils datasets methods base > >> > > >> > > >> > > >> > On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> > wrote: > >> > > >> >> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari < > yanadj28@gmail.com> > >> >> wrote: > >> >> > Sorry, I forgot to mention that the system will go to not > responding > >> >> > and > >> >> > need to be closed after the pop-up message appear. > >> >> > > >> >> > >> >> Please post the output of sessionInfo(), run it immediately before > the > >> >> command that causes the error. > >> >> > >> >> Thanks, > >> >> Dan > >> >> > >> >> > > >> >> > > >> >> > > >> >> > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> >> wrote: > >> >> >> > >> >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari > >> >> >> <yanadj28@gmail.com> > >> >> >> wrote: > >> >> >> > This error happen while I'm trying to view the example image. > >> >> >> > These is > >> >> >> > because I read from the manual, if I want to make sure that the > >> >> package > >> >> >> > is > >> >> >> > install correctly, it should be able to display the "lena.gif" > >> >> >> > image: > >> >> >> > > >> >> >> > > >> >> >> >>library("EBImage") > >> >> >> >>f = system.file("images", "lena.gif", package="EBImage") > >> >> >> >>lena = readImage(f) > >> >> >> >>display(lena) > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> Please post the output of > >> >> >> sessionInfo() > >> >> >> Thanks > >> >> >> Dan > >> >> >> > >> >> >> > >> >> >> > > >> >> >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum < > dtenenba@fhcrc.org> > >> >> >> > wrote: > >> >> >> >> > >> >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari > >> >> >> >> <yanadj28@gmail.com> > >> >> >> >> wrote: > >> >> >> >> > Hi, > >> >> >> >> > > >> >> >> >> > Please help me with these problem. Every time I'm trying to > >> >> >> >> > display > >> >> >> >> > the > >> >> >> >> > example image, I receive these kind of pop-up warning: > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically > >> >> >> >> > loaded > >> >> >> >> > modules > >> >> >> >> > were found. Pango will not work correctly. This probably > means > >> >> >> >> > there was an error in the creation of: > >> >> >> >> > 'C:\Windows\system32\etc\pango\pango.modules' > >> >> >> >> > You may be able to recreate this file by running > >> >> pango-querymodules. > >> >> >> >> > > >> >> >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: > >> >> >> >> > line > >> >> 1561 > >> >> >> >> > (g_object_ > >> >> >> >> > ref): assertion `G_IS_OBJECT (object)' failed > >> >> >> >> > > >> >> >> >> > ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line > 68 > >> >> >> >> > (_pango_engine_sh > >> >> >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > I have try several method that I found searching from the > >> >> >> >> > internet, > >> >> >> >> > but > >> >> >> >> > still I could not fix these problem. > >> >> >> >> > >> >> >> >> It's difficult for us to help without knowing the exact > commands > >> >> >> >> you > >> >> >> >> tried that caused this error, and more information about your > >> >> >> >> system > >> >> >> >> (e.g., the output of the sessionInfo() function). > >> >> >> >> > >> >> >> >> Dan > >> >> >> >> > >> >> >> >> > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > Nurdiyanah Bt Hj Jambari > >> >> >> >> > Student > >> >> >> >> > Faculty of Engineering > >> >> >> >> > Bachelor Engineering of Computer & Communication System > >> >> >> >> > Engineering > >> >> >> >> > University Putra Malaysia > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > -- > >> >> >> > Nurdiyanah Bt Hj Jambari > >> >> >> > Student > >> >> >> > Faculty of Engineering > >> >> >> > Bachelor Engineering of Computer & Communication System > >> >> >> > Engineering > >> >> >> > University Putra Malaysia > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Nurdiyanah Bt Hj Jambari > >> >> > Student > >> >> > Faculty of Engineering > >> >> > Bachelor Engineering of Computer & Communication System Engineering > >> >> > University Putra Malaysia > >> >> > >> > > >> > > >> > > >> > -- > >> > Nurdiyanah Bt Hj Jambari > >> > Student > >> > Faculty of Engineering > >> > Bachelor Engineering of Computer & Communication System Engineering > >> > University Putra Malaysia > >> > > >> > [[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 > > > > > > > > > > -- > > Nurdiyanah Bt Hj Jambari > > Student > > Faculty of Engineering > > Bachelor Engineering of Computer & Communication System Engineering > > University Putra Malaysia > > > > > > > > -- > > Nurdiyanah Bt Hj Jambari > > Student > > Faculty of Engineering > > Bachelor Engineering of Computer & Communication System Engineering > > University Putra Malaysia > -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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Nurdiyanah Jambari scripsit 03/07/2012 07:33 AM: > Can you please help me explain on how to place/install this GTK file. > I hope I didn't wrongly place it. I've been searching in the internet, but > there is no specific step for it. You do not need to search the internet, reading the documentation that comes with the EBImage package would be a relevant first step. Have you followed the steps described in the vignette "EBImage installation", Section "Windows"? Best wishes Wolfgang > > thank you. > > > On Wed, Mar 7, 2012 at 12:11 PM, Dan Tenenbaum<dtenenba at="" fhcrc.org=""> wrote: > >> On Tue, Mar 6, 2012 at 7:25 PM, Nurdiyanah Jambari<yanadj28 at="" gmail.com=""> >> wrote: >>> >>> >>> ---------- Forwarded message ---------- >>> From: Nurdiyanah Jambari<yanadj28 at="" gmail.com=""> >>> Date: Wed, Mar 7, 2012 at 10:50 AM >>> Subject: Re: [BioC] unable to readImage using EBImage package >>> To: Henrik Bengtsson<hb at="" biostat.ucsf.edu=""> >>> >>> >>>> library("EBImage") >>> >>>> sessionInfo() >>> R version 2.14.1 (2011-12-22) >>> Platform: i386-pc-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>> States.1252 LC_MONETARY=English_United States.1252 >>> LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] EBImage_3.10.0 abind_1.4-0 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.14.1 >>> >>> >>> >>> >> >> I have found that for Windows, EBImage does not like the most recent >> version of GTK+. >> You should install the version specified in the EBImage installation >> vignette: >> >> >> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle _2.16.6-20100912_win32.zip >> >> Dan >> >> >>> >>> >>> On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson<hb at="" biostat.ucsf.edu=""> >>> wrote: >>>> >>>> They're also interested in details about EBImage, so: >>>> >>>>> library("EBImage"); >>>>> sessionInfo(); >>>> >>>> Over and out. >>>> >>>> /Henrik >>>> >>>> On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari<yanadj28 at="" gmail.com=""> >>>> wrote: >>>>> Sorry, I miss understood your request. This is the output of my >>>>> sessionInfo(): >>>>> >>>>>> sessionInfo() >>>>> R version 2.14.1 (2011-12-22) >>>>> Platform: i386-pc-mingw32/i386 (32-bit) >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>> States.1252 LC_MONETARY=English_United States.1252 >>>>> LC_NUMERIC=C >>>>> [5] LC_TIME=English_United States.1252 >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> >>>>> >>>>> On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum<dtenenba at="" fhcrc.org=""> >>>>> wrote: >>>>> >>>>>> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari< >> yanadj28 at gmail.com> >>>>>> wrote: >>>>>>> Sorry, I forgot to mention that the system will go to not >> responding >>>>>>> and >>>>>>> need to be closed after the pop-up message appear. >>>>>>> >>>>>> >>>>>> Please post the output of sessionInfo(), run it immediately before >> the >>>>>> command that causes the error. >>>>>> >>>>>> Thanks, >>>>>> Dan >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum<dtenenba at="" fhcrc.org=""> >>>>>> wrote: >>>>>>>> >>>>>>>> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari >>>>>>>> <yanadj28 at="" gmail.com=""> >>>>>>>> wrote: >>>>>>>>> This error happen while I'm trying to view the example image. >>>>>>>>> These is >>>>>>>>> because I read from the manual, if I want to make sure that the >>>>>> package >>>>>>>>> is >>>>>>>>> install correctly, it should be able to display the "lena.gif" >>>>>>>>> image: >>>>>>>>> >>>>>>>>> >>>>>>>>>> library("EBImage") >>>>>>>>>> f = system.file("images", "lena.gif", package="EBImage") >>>>>>>>>> lena = readImage(f) >>>>>>>>>> display(lena) >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> Please post the output of >>>>>>>> sessionInfo() >>>>>>>> Thanks >>>>>>>> Dan >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum< >> dtenenba at fhcrc.org> >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari >>>>>>>>>> <yanadj28 at="" gmail.com=""> >>>>>>>>>> wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Please help me with these problem. Every time I'm trying to >>>>>>>>>>> display >>>>>>>>>>> the >>>>>>>>>>> example image, I receive these kind of pop-up warning: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ** (<unknown>:2932): WARNING **: No builtin or dynamically >>>>>>>>>>> loaded >>>>>>>>>>> modules >>>>>>>>>>> were found. Pango will not work correctly. This probably >> means >>>>>>>>>>> there was an error in the creation of: >>>>>>>>>>> 'C:\Windows\system32\etc\pango\pango.modules' >>>>>>>>>>> You may be able to recreate this file by running >>>>>> pango-querymodules. >>>>>>>>>>> >>>>>>>>>>> (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: >>>>>>>>>>> line >>>>>> 1561 >>>>>>>>>>> (g_object_ >>>>>>>>>>> ref): assertion `G_IS_OBJECT (object)' failed >>>>>>>>>>> >>>>>>>>>>> ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line >> 68 >>>>>>>>>>> (_pango_engine_sh >>>>>>>>>>> ape_shape): assertion `PANGO_IS_FONT (font)' failed >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I have try several method that I found searching from the >>>>>>>>>>> internet, >>>>>>>>>>> but >>>>>>>>>>> still I could not fix these problem. >>>>>>>>>> >>>>>>>>>> It's difficult for us to help without knowing the exact >> commands >>>>>>>>>> you >>>>>>>>>> tried that caused this error, and more information about your >>>>>>>>>> system >>>>>>>>>> (e.g., the output of the sessionInfo() function). >>>>>>>>>> >>>>>>>>>> Dan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Nurdiyanah Bt Hj Jambari >>>>>>>>>>> Student >>>>>>>>>>> Faculty of Engineering >>>>>>>>>>> Bachelor Engineering of Computer& Communication System >>>>>>>>>>> Engineering >>>>>>>>>>> University Putra Malaysia >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Nurdiyanah Bt Hj Jambari >>>>>>>>> Student >>>>>>>>> Faculty of Engineering >>>>>>>>> Bachelor Engineering of Computer& Communication System >>>>>>>>> Engineering >>>>>>>>> University Putra Malaysia >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Nurdiyanah Bt Hj Jambari >>>>>>> Student >>>>>>> Faculty of Engineering >>>>>>> Bachelor Engineering of Computer& Communication System Engineering >>>>>>> University Putra Malaysia >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Nurdiyanah Bt Hj Jambari >>>>> Student >>>>> Faculty of Engineering >>>>> Bachelor Engineering of Computer& Communication System Engineering >>>>> University Putra Malaysia >>>>> >>>>> [[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 >>> >>> >>> >>> >>> -- >>> Nurdiyanah Bt Hj Jambari >>> Student >>> Faculty of Engineering >>> Bachelor Engineering of Computer& Communication System Engineering >>> University Putra Malaysia >>> >>> >>> >>> -- >>> Nurdiyanah Bt Hj Jambari >>> Student >>> Faculty of Engineering >>> Bachelor Engineering of Computer& Communication System Engineering >>> University Putra Malaysia >> > > > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dan Tenenbaum ★ 8.2k
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On Fri, Mar 9, 2012 at 4:22 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > Hai, > I still not able to overcome my problem. I have already download the gtk > from the link that you give. > I'm still having the same warning/error. Can you help me? > > Did you remove the previous GTK+ installation from your system and your PATH? Did you add the new GTK+ installation to your PATH as documented in the EBImage vignette? Dan > > On Wed, Mar 7, 2012 at 2:33 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> > wrote: >> >> Can you please help me explain on how to place/install this GTK file. >> I hope I didn't wrongly place it. I've been searching in the internet, but >> there is no specific step for it. >> >> thank you. >> >> >> >> On Wed, Mar 7, 2012 at 12:11 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >>> >>> On Tue, Mar 6, 2012 at 7:25 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >>> wrote: >>> > >>> > >>> > ---------- Forwarded message ---------- >>> > From: Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >>> > Date: Wed, Mar 7, 2012 at 10:50 AM >>> > Subject: Re: [BioC] unable to readImage using EBImage package >>> > To: Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> >>> > >>> > >>> >> library("EBImage") >>> > >>> >> sessionInfo() >>> > R version 2.14.1 (2011-12-22) >>> > Platform: i386-pc-mingw32/i386 (32-bit) >>> > >>> > locale: >>> > [1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United >>> > States.1252??? LC_MONETARY=English_United States.1252 >>> > LC_NUMERIC=C >>> > [5] LC_TIME=English_United States.1252 >>> > >>> > attached base packages: >>> > [1] stats???? graphics? grDevices utils???? datasets? methods?? base >>> > >>> > other attached packages: >>> > [1] EBImage_3.10.0 abind_1.4-0 >>> > >>> > loaded via a namespace (and not attached): >>> > [1] tools_2.14.1 >>> > >>> > >>> > >>> > >>> >>> I have found that for Windows, EBImage does not like the most recent >>> version of GTK+. >>> You should install the version specified in the EBImage installation >>> vignette: >>> >>> >>> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundl e_2.16.6-20100912_win32.zip >>> >>> Dan >>> >>> >>> > >>> > >>> > On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> >>> > wrote: >>> >> >>> >> They're also interested in details about EBImage, so: >>> >> >>> >> > library("EBImage"); >>> >> > sessionInfo(); >>> >> >>> >> Over and out. >>> >> >>> >> /Henrik >>> >> >>> >> On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari >>> >> <yanadj28 at="" gmail.com=""> >>> >> wrote: >>> >> > Sorry, I miss understood your request. This is the output of my >>> >> > sessionInfo(): >>> >> > >>> >> >> sessionInfo() >>> >> > R version 2.14.1 (2011-12-22) >>> >> > Platform: i386-pc-mingw32/i386 (32-bit) >>> >> > >>> >> > locale: >>> >> > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United >>> >> > States.1252 ? ?LC_MONETARY=English_United States.1252 >>> >> > LC_NUMERIC=C >>> >> > [5] LC_TIME=English_United States.1252 >>> >> > >>> >> > attached base packages: >>> >> > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >> > >>> >> > >>> >> > >>> >> > On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>> >> > wrote: >>> >> > >>> >> >> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari >>> >> >> <yanadj28 at="" gmail.com=""> >>> >> >> wrote: >>> >> >> > Sorry, I forgot to mention that the system will go to not >>> >> >> > responding >>> >> >> > and >>> >> >> > need to be closed after the pop-up message appear. >>> >> >> > >>> >> >> >>> >> >> Please post the output of sessionInfo(), run it immediately before >>> >> >> the >>> >> >> command that causes the error. >>> >> >> >>> >> >> Thanks, >>> >> >> Dan >>> >> >> >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum >>> >> >> > <dtenenba at="" fhcrc.org=""> >>> >> >> wrote: >>> >> >> >> >>> >> >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari >>> >> >> >> <yanadj28 at="" gmail.com=""> >>> >> >> >> wrote: >>> >> >> >> > This error happen while I'm trying to view the example image. >>> >> >> >> > These is >>> >> >> >> > because I read from the manual, if I want to make sure that >>> >> >> >> > the >>> >> >> package >>> >> >> >> > is >>> >> >> >> > install correctly, it should be able to display the "lena.gif" >>> >> >> >> > image: >>> >> >> >> > >>> >> >> >> > >>> >> >> >> >>library("EBImage") >>> >> >> >> >>f = system.file("images", "lena.gif", package="EBImage") >>> >> >> >> >>lena = readImage(f) >>> >> >> >> >>display(lena) >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> Please post the output of >>> >> >> >> sessionInfo() >>> >> >> >> Thanks >>> >> >> >> Dan >>> >> >> >> >>> >> >> >> >>> >> >> >> > >>> >> >> >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum >>> >> >> >> > <dtenenba at="" fhcrc.org=""> >>> >> >> >> > wrote: >>> >> >> >> >> >>> >> >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari >>> >> >> >> >> <yanadj28 at="" gmail.com=""> >>> >> >> >> >> wrote: >>> >> >> >> >> > Hi, >>> >> >> >> >> > >>> >> >> >> >> > Please help me with these problem. Every time I'm trying to >>> >> >> >> >> > display >>> >> >> >> >> > the >>> >> >> >> >> > example image, I receive these kind of pop-up warning: >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > ** (<unknown>:2932): WARNING **: No builtin or dynamically >>> >> >> >> >> > loaded >>> >> >> >> >> > modules >>> >> >> >> >> > were found. Pango will not work correctly. This probably >>> >> >> >> >> > means >>> >> >> >> >> > there was an error in the creation of: >>> >> >> >> >> > ? 'C:\Windows\system32\etc\pango\pango.modules' >>> >> >> >> >> > You may be able to recreate this file by running >>> >> >> pango-querymodules. >>> >> >> >> >> > >>> >> >> >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c: >>> >> >> >> >> > line >>> >> >> 1561 >>> >> >> >> >> > (g_object_ >>> >> >> >> >> > ref): assertion `G_IS_OBJECT (object)' failed >>> >> >> >> >> > >>> >> >> >> >> > ** (<unknown>:2932): CRITICAL **: file pango- engine.c: line >>> >> >> >> >> > 68 >>> >> >> >> >> > (_pango_engine_sh >>> >> >> >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > I have try several method that I found searching from the >>> >> >> >> >> > internet, >>> >> >> >> >> > but >>> >> >> >> >> > still I could not fix these problem. >>> >> >> >> >> >>> >> >> >> >> It's difficult for us to help without knowing the exact >>> >> >> >> >> commands >>> >> >> >> >> you >>> >> >> >> >> tried that caused this error, and more information about your >>> >> >> >> >> system >>> >> >> >> >> (e.g., the output of the sessionInfo() function). >>> >> >> >> >> >>> >> >> >> >> Dan >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > Nurdiyanah Bt Hj Jambari >>> >> >> >> >> > Student >>> >> >> >> >> > Faculty of Engineering >>> >> >> >> >> > Bachelor Engineering of Computer & Communication System >>> >> >> >> >> > Engineering >>> >> >> >> >> > University Putra Malaysia >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > -- >>> >> >> >> > Nurdiyanah Bt Hj Jambari >>> >> >> >> > Student >>> >> >> >> > Faculty of Engineering >>> >> >> >> > Bachelor Engineering of Computer & Communication System >>> >> >> >> > Engineering >>> >> >> >> > University Putra Malaysia >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > -- >>> >> >> > Nurdiyanah Bt Hj Jambari >>> >> >> > Student >>> >> >> > Faculty of Engineering >>> >> >> > Bachelor Engineering of Computer & Communication System >>> >> >> > Engineering >>> >> >> > University Putra Malaysia >>> >> >> >>> >> > >>> >> > >>> >> > >>> >> > -- >>> >> > Nurdiyanah Bt Hj Jambari >>> >> > Student >>> >> > Faculty of Engineering >>> >> > Bachelor Engineering of Computer & Communication System Engineering >>> >> > University Putra Malaysia >>> >> > >>> >> > ? ? ? ?[[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 >>> > >>> > >>> > >>> > >>> > -- >>> > Nurdiyanah Bt Hj Jambari >>> > Student >>> > Faculty of Engineering >>> > Bachelor Engineering of Computer & Communication System Engineering >>> > University Putra Malaysia >>> > >>> > >>> > >>> > -- >>> > Nurdiyanah Bt Hj Jambari >>> > Student >>> > Faculty of Engineering >>> > Bachelor Engineering of Computer & Communication System Engineering >>> > University Putra Malaysia >> >> >> >> >> -- >> Nurdiyanah Bt Hj Jambari >> Student >> Faculty of Engineering >> Bachelor Engineering of Computer & Communication System Engineering >> University Putra Malaysia > > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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Dan Tenenbaum ★ 8.2k
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On Sat, Mar 10, 2012 at 10:21 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > Hi, could you explain what is EBImage vignette? > > http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/d oc/EBImage-installation.pdf Also http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/d oc/EBImage-introduction.pdf http://bioconductor.org/packages/release/bioc/manuals/EBImage/man/EBIm age.pdf All these links come from: http://bioconductor.org/packages/release/bioc/html/EBImage.html You can also do this within R: browseVignettes(package="EBImage") Dan > > On Sat, Mar 10, 2012 at 1:28 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Fri, Mar 9, 2012 at 4:22 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> wrote: >> > Hai, >> > I still not able to overcome my problem. I have already download the gtk >> > from the link that you give. >> > I'm still having the same warning/error. Can you help me? >> > >> > >> >> Did you remove the previous GTK+ installation from your system and your >> PATH? >> Did you add the new GTK+ installation to your PATH as documented in >> the EBImage vignette? >> Dan >> >> >> > >> > On Wed, Mar 7, 2012 at 2:33 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> > wrote: >> >> >> >> Can you please help me explain on how to place/install this GTK file. >> >> I hope I didn't wrongly place it. I've been searching in the internet, >> >> but >> >> there is no specific step for it. >> >> >> >> thank you. >> >> >> >> >> >> >> >> On Wed, Mar 7, 2012 at 12:11 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> wrote: >> >>> >> >>> On Tue, Mar 6, 2012 at 7:25 PM, Nurdiyanah Jambari >> >>> <yanadj28 at="" gmail.com=""> >> >>> wrote: >> >>> > >> >>> > >> >>> > ---------- Forwarded message ---------- >> >>> > From: Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> >> >>> > Date: Wed, Mar 7, 2012 at 10:50 AM >> >>> > Subject: Re: [BioC] unable to readImage using EBImage package >> >>> > To: Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> >> >>> > >> >>> > >> >>> >> library("EBImage") >> >>> > >> >>> >> sessionInfo() >> >>> > R version 2.14.1 (2011-12-22) >> >>> > Platform: i386-pc-mingw32/i386 (32-bit) >> >>> > >> >>> > locale: >> >>> > [1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United >> >>> > States.1252??? LC_MONETARY=English_United States.1252 >> >>> > LC_NUMERIC=C >> >>> > [5] LC_TIME=English_United States.1252 >> >>> > >> >>> > attached base packages: >> >>> > [1] stats???? graphics? grDevices utils???? datasets? methods?? base >> >>> > >> >>> > other attached packages: >> >>> > [1] EBImage_3.10.0 abind_1.4-0 >> >>> > >> >>> > loaded via a namespace (and not attached): >> >>> > [1] tools_2.14.1 >> >>> > >> >>> > >> >>> > >> >>> > >> >>> >> >>> I have found that for Windows, EBImage does not like the most recent >> >>> version of GTK+. >> >>> You should install the version specified in the EBImage installation >> >>> vignette: >> >>> >> >>> >> >>> >> >>> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bu ndle_2.16.6-20100912_win32.zip >> >>> >> >>> Dan >> >>> >> >>> >> >>> > >> >>> > >> >>> > On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson >> >>> > <hb at="" biostat.ucsf.edu=""> >> >>> > wrote: >> >>> >> >> >>> >> They're also interested in details about EBImage, so: >> >>> >> >> >>> >> > library("EBImage"); >> >>> >> > sessionInfo(); >> >>> >> >> >>> >> Over and out. >> >>> >> >> >>> >> /Henrik >> >>> >> >> >>> >> On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari >> >>> >> <yanadj28 at="" gmail.com=""> >> >>> >> wrote: >> >>> >> > Sorry, I miss understood your request. This is the output of my >> >>> >> > sessionInfo(): >> >>> >> > >> >>> >> >> sessionInfo() >> >>> >> > R version 2.14.1 (2011-12-22) >> >>> >> > Platform: i386-pc-mingw32/i386 (32-bit) >> >>> >> > >> >>> >> > locale: >> >>> >> > [1] LC_COLLATE=English_United States.1252 >> >>> >> > ?LC_CTYPE=English_United >> >>> >> > States.1252 ? ?LC_MONETARY=English_United States.1252 >> >>> >> > LC_NUMERIC=C >> >>> >> > [5] LC_TIME=English_United States.1252 >> >>> >> > >> >>> >> > attached base packages: >> >>> >> > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> >>> >> > base >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum >> >>> >> > <dtenenba at="" fhcrc.org=""> >> >>> >> > wrote: >> >>> >> > >> >>> >> >> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari >> >>> >> >> <yanadj28 at="" gmail.com=""> >> >>> >> >> wrote: >> >>> >> >> > Sorry, I forgot to mention that the system will go to not >> >>> >> >> > responding >> >>> >> >> > and >> >>> >> >> > need to be closed after the pop-up message appear. >> >>> >> >> > >> >>> >> >> >> >>> >> >> Please post the output of sessionInfo(), run it immediately >> >>> >> >> before >> >>> >> >> the >> >>> >> >> command that causes the error. >> >>> >> >> >> >>> >> >> Thanks, >> >>> >> >> Dan >> >>> >> >> >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum >> >>> >> >> > <dtenenba at="" fhcrc.org=""> >> >>> >> >> wrote: >> >>> >> >> >> >> >>> >> >> >> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari >> >>> >> >> >> <yanadj28 at="" gmail.com=""> >> >>> >> >> >> wrote: >> >>> >> >> >> > This error happen while I'm trying to view the example >> >>> >> >> >> > image. >> >>> >> >> >> > These is >> >>> >> >> >> > because I read from the manual, if I want to make sure that >> >>> >> >> >> > the >> >>> >> >> package >> >>> >> >> >> > is >> >>> >> >> >> > install correctly, it should be able to display the >> >>> >> >> >> > "lena.gif" >> >>> >> >> >> > image: >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> >>library("EBImage") >> >>> >> >> >> >>f = system.file("images", "lena.gif", package="EBImage") >> >>> >> >> >> >>lena = readImage(f) >> >>> >> >> >> >>display(lena) >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> Please post the output of >> >>> >> >> >> sessionInfo() >> >>> >> >> >> Thanks >> >>> >> >> >> Dan >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> > >> >>> >> >> >> > On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum >> >>> >> >> >> > <dtenenba at="" fhcrc.org=""> >> >>> >> >> >> > wrote: >> >>> >> >> >> >> >> >>> >> >> >> >> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari >> >>> >> >> >> >> <yanadj28 at="" gmail.com=""> >> >>> >> >> >> >> wrote: >> >>> >> >> >> >> > Hi, >> >>> >> >> >> >> > >> >>> >> >> >> >> > Please help me with these problem. Every time I'm trying >> >>> >> >> >> >> > to >> >>> >> >> >> >> > display >> >>> >> >> >> >> > the >> >>> >> >> >> >> > example image, I receive these kind of pop-up warning: >> >>> >> >> >> >> > >> >>> >> >> >> >> > >> >>> >> >> >> >> > ** (<unknown>:2932): WARNING **: No builtin or >> >>> >> >> >> >> > dynamically >> >>> >> >> >> >> > loaded >> >>> >> >> >> >> > modules >> >>> >> >> >> >> > were found. Pango will not work correctly. This probably >> >>> >> >> >> >> > means >> >>> >> >> >> >> > there was an error in the creation of: >> >>> >> >> >> >> > ? 'C:\Windows\system32\etc\pango\pango.modules' >> >>> >> >> >> >> > You may be able to recreate this file by running >> >>> >> >> pango-querymodules. >> >>> >> >> >> >> > >> >>> >> >> >> >> > (<unknown>:2932): GLib-GObject-CRITICAL **: file >> >>> >> >> >> >> > gobject.c: >> >>> >> >> >> >> > line >> >>> >> >> 1561 >> >>> >> >> >> >> > (g_object_ >> >>> >> >> >> >> > ref): assertion `G_IS_OBJECT (object)' failed >> >>> >> >> >> >> > >> >>> >> >> >> >> > ** (<unknown>:2932): CRITICAL **: file pango- engine.c: >> >>> >> >> >> >> > line >> >>> >> >> >> >> > 68 >> >>> >> >> >> >> > (_pango_engine_sh >> >>> >> >> >> >> > ape_shape): assertion `PANGO_IS_FONT (font)' failed >> >>> >> >> >> >> > >> >>> >> >> >> >> > >> >>> >> >> >> >> > I have try several method that I found searching from >> >>> >> >> >> >> > the >> >>> >> >> >> >> > internet, >> >>> >> >> >> >> > but >> >>> >> >> >> >> > still I could not fix these problem. >> >>> >> >> >> >> >> >>> >> >> >> >> It's difficult for us to help without knowing the exact >> >>> >> >> >> >> commands >> >>> >> >> >> >> you >> >>> >> >> >> >> tried that caused this error, and more information about >> >>> >> >> >> >> your >> >>> >> >> >> >> system >> >>> >> >> >> >> (e.g., the output of the sessionInfo() function). >> >>> >> >> >> >> >> >>> >> >> >> >> Dan >> >>> >> >> >> >> >> >
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Hi, I have done all the steps suggested but still not able to fix this problem. Is it true that if I'm not able to open "lena.gif" that meaning the package is not install correctly and I wont able to open any other image from my own files? ** (<unknown>:1204): WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: 'C:\Windows\system32\etc\pango\pango.modules' You may be able to recreate this file by running pango-querymodules. (<unknown>:1204): GLib-GObject-CRITICAL **: file gobject.c: line 1561 (g_object_ ref): assertion `G_IS_OBJECT (object)' failed ** (<unknown>:1204): CRITICAL **: file pango-engine.c: line 68 (_pango_engine_sh ape_shape): assertion `PANGO_IS_FONT (font)' failed Can you help me explain what is the correct command to call an image, for example I have an image name "user186g1.tif", it is located in "D:\FYP\image". Below is the current output of my sessionInfo(EBImage): R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: character(0) other attached packages: [1] EBImage_3.10.0 loaded via a namespace (and not attached): [1] base_2.14.1 graphics_2.14.1 grDevices_2.14.1 methods_2.14.1 stats_2.14.1 utils_2.14.1 thank you. -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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On Tue, Mar 13, 2012 at 7:42 AM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > Hi, > > I have done all the steps suggested but still not able to fix this problem. > Is it true that if I'm not able to open "lena.gif" that meaning the package > is not install correctly and I wont able to open any other image from my own > files? > It's probably the case that if you can't run functions on sample images, you won't be able to run them on your own images. > ** (<unknown>:1204): WARNING **: No builtin or dynamically loaded modules > > were found. Pango will not work correctly. This probably means > there was an error in the creation of: > ? 'C:\Windows\system32\etc\pango\pango.modules' > You may be able to recreate this file by running pango-querymodules. > > (<unknown>:1204): GLib-GObject-CRITICAL **: file gobject.c: line 1561 > (g_object_ > > ref): assertion `G_IS_OBJECT (object)' failed > > ** (<unknown>:1204): CRITICAL **: file pango-engine.c: line 68 > (_pango_engine_sh > > ape_shape): assertion `PANGO_IS_FONT (font)' failed > > What command caused this error? Sending error messages without the commands that caused them is not too useful. > Can you help me explain what is the correct command to call an image, for > example I have an image name "user186g1.tif", > it is located in "D:\FYP\image". What is the command you are trying to run? For readImage(), instead of doing this: > f = system.file("images", "lena.gif", package="EBImage") > lena = readImage(f) Do this: readImage("d:/FYP/image/user186g1.tif") system.file() is used to refer to files that are part of installed packages. When you want to refer to your own files, you can usually just put in the full path to your file instead of the system.file() function. Dan > > Below is the current output of my sessionInfo(EBImage): > > > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United > States.1252??? LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > character(0) > > > other attached packages: > [1] EBImage_3.10.0 > > loaded via a namespace (and not attached): > [1] base_2.14.1????? graphics_2.14.1? grDevices_2.14.1 methods_2.14.1 > stats_2.14.1???? utils_2.14.1 > > thank you. > > > > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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I have run this command: >library("EBImage") >f = system.file("images", "lena.gif", package="EBImage") >lena = readImage(f) >display(lena) the error received: > ** (<unknown>:1204): WARNING **: No builtin or dynamically loaded modules > > were found. Pango will not work correctly. This probably means > there was an error in the creation of: > 'C:\Windows\system32\etc\ pango\pango.modules' > You may be able to recreate this file by running pango-querymodules. > > (<unknown>:1204): GLib-GObject-CRITICAL **: file gobject.c: line 1561 > (g_object_ > > ref): assertion `G_IS_OBJECT (object)' failed > > ** (<unknown>:1204): CRITICAL **: file pango-engine.c: line 68 > (_pango_engine_sh > > ape_shape): assertion `PANGO_IS_FONT (font)' failed I have tried this command you gave me: >readImage("d:/FYP/image/user186g1.tif") the result, my R is stop working and need to be stop and close. Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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On Tue, Mar 13, 2012 at 5:41 PM, Nurdiyanah Jambari <yanadj28 at="" gmail.com=""> wrote: > I have run this command: > >>library("EBImage") > >>f = system.file("images", "lena.gif", package="EBImage") >>lena = readImage(f) >>display(lena) > > the error received: > > >> ** (<unknown>:1204): WARNING **: No builtin or dynamically loaded modules >> >> were found. Pango will not work correctly. This probably means >> there was an error in the creation of: >> ? 'C:\Windows\system32\etc\ > pango\pango.modules' >> You may be able to recreate this file by running pango- querymodules. >> >> (<unknown>:1204): GLib-GObject-CRITICAL **: file gobject.c: line 1561 >> (g_object_ >> >> ref): assertion `G_IS_OBJECT (object)' failed >> >> ** (<unknown>:1204): CRITICAL **: file pango-engine.c: line 68 >> (_pango_engine_sh >> >> ape_shape): assertion `PANGO_IS_FONT (font)' failed > > I have tried this command you gave me: > >>readImage("d:/FYP/image/user186g1.tif") > > the result, my R is stop working and need to be stop and close. > > I think we are going around in circles. Did you verify that the correct version of GTK+ (i.e., not the newest version) is installed ad added to the PATH, and that the newest version has been uninstalled and removed from the PATH, as I suggested earlier? How did you install the file http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_2. 16.6-20100912_win32.zip ? Dan > > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia
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@nurdiyanah-jambari-4934
Last seen 6.6 years ago
Hai, I think I'll give up with the EBImage package and I've already try the rtiff package. I can open the .tiff image using these package. Now I have problem to find a a filter package for the image filtering step. Most of the filter I found, stated that it is a filter of 'time series'. How can I use these filter for my .tiff image? Filter package that I'm trying to look at is mFilter package and robfilter package. I also need to use the wavelets package in this project. On Wed, Mar 14, 2012 at 10:30 AM, Nurdiyanah Jambari <yanadj28@gmail.com>wrote: > I have already uninstall everything and start from zero. I install again R > (R-2.14.1), imagemagick (ImageMagick-6.7.5-Q16), EBImage (from the > bioconductor web page) and the GTK file that you suggest > (gtk+-bundle_2.16.6-20100912_win32). I place the GTK file in "C:\opt\gtk" > from what i read inside the README from inside the package. The > "gtk-demo.exe" can be run without error. > Is this correct? > > > > I think we are going around in circles. >> Did you verify that the correct version of GTK+ (i.e., not the newest >> version) is installed ad added to the PATH, and that the newest >> version has been uninstalled and removed from the PATH, as I suggested >> earlier? >> >> How did you install the file >> >> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle _2.16.6-20100912_win32.zip >> >> ? >> Dan >> > > -- > Nurdiyanah Bt Hj Jambari > Student > Faculty of Engineering > Bachelor Engineering of Computer & Communication System Engineering > University Putra Malaysia > -- Nurdiyanah Bt Hj Jambari Student Faculty of Engineering Bachelor Engineering of Computer & Communication System Engineering University Putra Malaysia [[alternative HTML version deleted]]
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