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 use xcms online a lot lately. As it is not yet possible to compare 4 groups yet, I have also used the regular version of xcms on my PC. This alloows me to get EIC's in which the data of 4 groups is plotted. I do, however, not get the same (order of) results using both approaches. I initially thought that this might be due to the fact that I included additional samples to the obiwarp retention time correction step, but also analysing exactly the same two groups, I do not get the same results. I checked the settings of both methods, but did not find differences. The only thing I am not sure of is the the Alignment settings: xcms used "peakgroups", I thought this was the "density" algoritm. I expect I am overlooking something. Maybe someone else can find what I am doing wrong here:
I am currently using XCMS online for most of my data analysis. To speed up identification, it would be nice to use the Camera package for identification of common "neutral losses", or other specific fragments. Are you planning to add functionality to XCMS online that would allow to screen for such common fragments? Presently the functionality of Camera within XCMS online is still relatively limited.
I am struggeling a bit with making new methods in XCMS online. I currenly have a long list of slighly modified methods. Sometimes I just want to change some settings without changing the name of the method. I could however not figure out how this should be done: If I make a change in the method, the button "save current" is not appearing. In addition, first pressing the button "create new" and afterwards saving the method under the same name doesn't work either. It is probably something trivial that I have missed. A related question that I have is how I should remove methods that I do not use anymore. Sometimes I see a button "delete", but is is not always pressent.
on which basis does the CAMERA package determine the charge of a metabolite? I have got the impression that it does not always correctly determine the charge of metabolites. Does this heavily rely on matching of the EICs of isotopes? I have attached an excel sheet of an annotated diffreport of a metabolite group of which I think the annotation of the charge was incorrect. The data has been generated using XCMS online.
I installed metaXCMS a few days ago and I have the following problem running it: before installing metaXCMS I completely removed R and all packages from my PC before reinstalling R, XCMS, metaXCMS and all dependencies. After the new installation metaXCMS worked fine the first time. However, after quitting R and starting a new metaXCMS session I got the following error:
> library(metaXCMS) Loading required package: cairoDevice Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/Program Files/R/R-2.13.1/library/cairoDevice/libs/i386/cairoDevice.dll': LoadLibrary failure: The specified module could not be found.
Error: package 'cairoDevice' could not be loaded
Are there plans to integrate metaXCMS into the online version of XCMS?
I just had a look at the results within a feature group. The retention time differences within the feature groups are similar (as expecxted). I found it strange however, to see that the fold change differences for features within a feature groups differed between the datasets analysed, whereas I had expected that features coming from the same analyte would give similar changes.
Hi, I just got the results of my first XCMS online analysis and it worked like a charm. I have two question about the presentation of the results in the results table: 1) In the "feature group" features with very different retention times are assigned to the same feature group. e.g. a particular feauture group contains features with retention times ranging from 16 to 51 minutes. How is that possible? I thougth that one of the criteria to be grouped in one feature group was that the features should have the same retention time. 2) to what do the numbers between the square brackets [] in the column "isotopes" refer?
Great site! I just tried to analyse some data with XCMS online (ID 1484). Uploading the data seemed to go ok. After submitting the job, analysis stops after 50% of the data has been processed (feauture detection done (40%), retention time correction done (50%), creating diffreport and EICs (50%), thereafter I get the message under status "XCMS processing failed". So I think the online version of XCMS crashes during the generation of the diffreport and EICs. I can however, not open the error message. I am using Windows XP and IE7.
