Hi Ralf, I got around the problem of R repeatedly asking for the installation of GTK+. It turned out to be a version problem: On OSX 10.8.3 you need the GTK_2.24.17-X11 package (not the GTK 2.18.5-X11 that automatically loads. I still do not succeed in installing metaXCMS. It tends to install, as I just see a flash of metaXCMS, but this window quickly disappears after opening, generating in the following error message:
Loading required package: sp * installing *source* package ‘metaXCMS’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded sh: line 1: 775 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 < /var/folders/0s/ym2z5zqs7n301k1l1zvpb4dr0000gp/T//Rtmp6EkMJr/file3053799c556
*** caught segfault *** address 0x0, cause 'memory not mapped'
I just tried to install metaXCMS on my new Mac (OSX 10.8.3, R3.0.0). I did however not succeed. I followed the installation guidelines given on the scripps website. I guess it has something to do with the loading of the GTK+ package: after installing this package after loading the cairodevice, other packages in R keep on asking to install the GTK+ package and metaXCMS does not install. This is what I get:
'.find.package' is deprecated. Use 'find.package' instead. See help("Deprecated") Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so Reason: image not found trying URL 'http://r.research.att.com/libs/GTK_2.18.5-X11.pkg' Content type 'text/plain' length 59914166 bytes (57.1 Mb) opened URL ================================================= downloaded 57.1 Mb
Learn more about GTK+ at http://www.gtk.org If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN starting httpd help server ... done Loading required package: sp Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so Reason: image not found In addition: Warning message: In fun(libname, pkgname) : Failed to load cairoDevice, attempting to install itError in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so Reason: image not found
Learn more about GTK+ at http://www.gtk.org If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Loading required package: xlsxjars Loading required package: rJava * installing *source* package ‘metaXCMS’ ... ** R ** inst ** preparing package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so Reason: image not found Warning in fun(libname, pkgname) : Failed to load cairoDevice, attempting to install itError in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so Reason: image not found
Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so Reason: image not found Warning: Failed to load RGtk2 dynamic library, attempting to install it. Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so Reason: image not found Warning in fun(libname, pkgname) : Failed to load cairoDevice, attempting to install itError in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so Reason: image not found
Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so Reason: image not found Warning: Failed to load RGtk2 dynamic library, attempting to install it. Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error : .onAttach failed in attachNamespace() for 'metaXCMS', details: call: .Call(name, ..., PACKAGE = PACKAGE) error: "S_gtk_window_new" not available for .Call() for package "RGtk2" Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/metaXCMS’
I was wondering whether it is possible to compare more than 2 groups. I have one "test" group and two control groups that I would like to compare. I am most interested in features that differ between the "test group" and both control groups. Now I manually check many EICs to see whether this is the case. It would be somewhat easier if I could have diffreport select these features for me. Extracting these features from the results file generated by "diffreport" is of course relatively easy, but I would then still get many box plots and EICs of features in which I am not so much interested.
Hi, just a question about the peaks that will be presented in the tsv generated by the diffreport. I am comparing two groups (each having 3 samples). When I manually checked for the presence of a specific peak in one of the groups, I found it to be present in all samples of this group. Also the peak shape looked ok: peakwidth approximately 15 seconds and the retention time deviation between the samples was max 10 sec (determined at the apex of the peak). It's not a very abundant peak but clearly present (>10 scans, intensity > 1000 cpm). This is the script I used:
Although the difference between the two groups was not statistically significant for this peak, I was expecting to find it at least back in the results.tsv file. Or am I wrong here?
Koen
p.s. I know that the peakwidth preferably should be something like c(15,90), but this also did not work out for this peak.
Hi, The EICs of the diffreport are coming with a title showing its m/z ratio range. The default setting gives these m/z ratios with 2 decimals. Is there an easy way to increase number of decimals in the title of the EICs? Koen
I installed metaXCMS on another Mac without any problems. So I decided to completely remove R from my Mac and reinstall everything. Upon reinstalling R/xcms and metaXCMS, the same problem occured: R crashed during loading of the cairoDevice. Can it be that this has something to do with the fact that GTK+ is already installed on my Mac? If so, how can I remove this before reinstallation?
Hi Kevin, following your suggestions R crashes while loading the cairoDevice in the package manager. R does also not ask to install GTK+. any idea why this is? Koen
I tried to install it via the GUI: via the "Package Installer". This dis not work and made R to crash. I just tried to install metaXCMS via the console using the command line, but I got the error "Warning: invalid package 'metaXCMS_0.1.19.tar.gz'" and "Error: ERROR: no packages specified". Should I put these packages in a specific directory?
Yes, the number of features detected still slightly differs from those detected by XCMS online. They do actually not differ from those detected by XCMS version 1.26.1.
I used xcms 1.26.1, which I thought is the latest stable version. The number of peaks detected by xcms are: Slco-1.mzXML 5160 Slco-2.mzXML 5190 Slco-3.mzXML 5300 Slco-4.mzXML 5070 Slco-5.mzXML 5306 FVB-1.mzXML 4641 FVB-2.mzXML 3905 FVB-3.mzXML 4116 FVB-4.mzXML 3214 FVB-5.mzXML 4272
So the number of features detected per sample differs slightly from those detected by XCMS online. The retention time deviation curves are however remarkably similar.Is it possible to use the ProfStepPad() instead of the Obiwarp? What exactly is the difference?
Do you have an idea about the cause of the large difference in differentially regulated features between XCMS and XCMS online? In addition, does the way in which XCMS does the peak picking changes from version to version?
