Hi Wolfgang Thanks again. I tried, but I still get an error saying that Cairo cannot generate an executable (or something in that line). I compiled all libraries manually. I contacted our HPC provided and they will set me up with a newer distro of OpenSUSE so I can use this one instead. Thanks a lot for all the help. I keep you posted if I find any problems or have any comments on the package, which looks great BTW. Cheers Paulo On 2011-02-13, at 5:46 PM, Wolfgang Huber wrote: > Dear Paulo > > sorry - that was my mistake. You were right to ask that question. I had overlooked that the source version of the Cairo R package *does* of course look for cairo libraries on your system. > > I don't have a CentOS system to test this, but assuming that you use bash, have you tried something like: > > env CAIRO_CFLAGS="-D_REENTRANT -I/opt/local/include/cairo -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng14" CAIRO_LIBS="-L/opt/local/lib -lfreetype -lpng14 -lz -lXrender -lcairo -lX11" R CMD INSTALL Downloads/Cairo_1.4-6.tar.gz > > This is all in one line, and the values between the "..." apply to my (Mac OS X with Mac ports) system, you'd need to replace the paths and library names with those applicable on your CentOS. > > Sorry that this is so painful... > > Wolfgang > > > Il Feb/13/11 7:36 PM, Paulo Nuin ha scritto: >> Hi Wolfgang >> >> I know what you mean. If I try to install Cairo (the BioC package) it compiles fine, but it still relies on the cairographics that it's installed in the system: >> >>> biocLite("Cairo") >> ... >> checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender >> configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12 >> ? >> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Cairo.so cairobem.o cairogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf- backend.o ps-backend.o svg-backend.o w32-backend.o xlib-backend.o -lfreetype -lfontconfig -lpng12 -lz -lXrender -lcairo -lX11 -ljpeg -ltiff >> installing to /home/nuin/R/x86_64-unknown-linux-gnu- library/2.13/Cairo/libs >> ** R >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices ... >> ** testing if installed package can be loaded >> >> * DONE (Cairo) >> >> CentOS "official" cairographics is 1.2.4, which is quite old. I'm not able to install a newer cairographics in /usr or I can break my system. I can compile another newer version of cairographics on /opt, but them I would have to make the BioC's Cairo to point to /opt include and library dirs. >> >> Thanks again >> >> Paulo >> >> >> >> On 2011-02-13, at 6:22 AM, Wolfgang Huber wrote: >> >>> Paulo >>> >>> perhaps you are trying to make things more complicated than necessary. >>> What happens when you enter >>> >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("Cairo") >>> >>> into your R command line? >>> >>> I am not sure what you mean by 'official package', the package page on CRAN, http://cran.r-project.org/web/packages/Cairo/index.html, provides 1.4-6. I noted though that older versions are sticking around on the internet. Also note that the "Cairo" R package is not the same as the "cairo graphics library" e.g. at http://www.cairographics.org. You should not need to put anything into /opt or point R to it or anything like that. >>> >>> Best wishes >>> Wolfgang >>> >>> >>> >>> >>> >>> >>> Il Feb/13/11 12:16 AM, Paulo Nuin ha scritto: >>>> Hi Wolfgang >>>> >>>> I'm not able to install a newer version on my CentOS. The only >>>> official package for Cairo is 1.2.4. I didn't find a way to compile R >>>> and point it to a locally compiled Cairo (in /opt) and I don't know >>>> if it's possible to manage the compilation of packages in order to >>>> use this Cairo compile too. >>>> >>>> Thanks >>>> >>>> Paulo >>>> >>>> >>>> >>>> On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote: >>>> >>>>> Dear Paulo >>>>> >>>>> Can you try with a more recent "Cairo" package (i.e. 1.4-6)? >>>>> >>>>> Wolfgang >>>>> >>>>> Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto: >>>>>> Hi Wolfgang >>>>>> >>>>>> Here's just after running ReadAffy: >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.13.0 Under development (unstable) (2011-01-30 >>>>>> r54169) Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] >>>>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] >>>>>> LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] >>>>>> LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C >>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>> LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: [1] stats graphics grDevices utils >>>>>> datasets methods base >>>>>> >>>>>> other attached packages: [1] arrayQualityMetrics_3.4.8 >>>>>> affy_1.29.2 [3] Biobase_2.11.8 >>>>>> >>>>>> loaded via a namespace (and not attached): [1] affyio_1.19.4 >>>>>> affyPLM_1.27.6 annotate_1.29.2 [4] AnnotationDbi_1.13.13 >>>>>> beadarray_2.1.10 Biostrings_2.19.9 [7] Cairo_1.4-5 >>>>>> cluster_1.13.2 DBI_0.2-5 [10] genefilter_1.33.0 >>>>>> grid_2.13.0 Hmisc_3.8-3 [13] hwriter_1.3 >>>>>> IRanges_1.9.21 lattice_0.19-17 [16] latticeExtra_0.6-14 >>>>>> limma_3.7.22 marray_1.29.1 [19] preprocessCore_1.13.5 >>>>>> RColorBrewer_1.0-2 RJSONIO_0.4-1 [22] RSQLite_0.9-4 >>>>>> setRNG_2009.11-1 splines_2.13.0 [25] survival_2.36-2 >>>>>> SVGAnnotation_0.7-2 tools_2.13.0 [28] vsn_3.19.3 >>>>>> XML_3.2-0 xtable_1.5-6 >>>>>> >>>>>> after running arrayQualityMetrics the only difference is the >>>>>> addition of hgu133plus2cdf_2.7.0 to the list. >>>>>> >>>>>> Thanks again >>>>>> >>>>>> Paulo >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote: >>>>>> >>>>>>> Dear Paulo >>>>>>> >>>>>>> what's your sessionInfo()? >>>>>>> >>>>>>> Wolfgang >>>>>>> >>>>>>> Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto: >>>>>>>> Hi Wolfgang >>>>>>>> >>>>>>>> Indeed, if I create an X11 tunnel, everything turns ok on the >>>>>>>> X11 side. My mistake, as the system is remote and some of the >>>>>>>> tests we run on a local machine. >>>>>>>> >>>>>>>> Nonetheless, we still find a problem at the end of the run, >>>>>>>> and it's similar to what we experienced the first time. Here >>>>>>>> is the error and traceback: >>>>>>>> >>>>>>>> >>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>>> force=T) >>>>>>>> The report will be written into directory 'quality'. Error in >>>>>>>> UseMethod("xmlAttrs", node) : no applicable method for >>>>>>>> 'xmlAttrs' applied to an object of class "NULL" >>>>>>>>> traceback() >>>>>>>> 16: xmlAttrs(node, addNamespace) 15: >>>>>>>> xmlGetAttr(clipPath[["path"]], "d") 14: >>>>>>>> getRect(xmlGetAttr(clipPath[["path"]], "d")) 13: >>>>>>>> getPlotRegion(n) 12: FUN(X[[1L]], ...) 11: lapply(X, FUN, >>>>>>>> ...) 10: sapply(tmp, function(n) all(getPlotRegion(n) == >>>>>>>> vb)) 9: getPlotRegionNodes(doc) 8: is.vector(X) 7: >>>>>>>> lapply(getPlotRegionNodes(doc), getPlotPoints) 6: >>>>>>>> getPlotPoints.XMLInternalDocument(doc) 5: >>>>>>>> annotationInfo at getPlotObjNodes(doc) 4: annotateSvgPlot(infile >>>>>>>> = svgtemp, outfile = nameimg, outdir = outdir, annotationInfo >>>>>>>> = module at svg, name = name) 3: reportModule(p = p, module = >>>>>>>> modules[[i]], currentIndex = currentIndex, arrayTable = >>>>>>>> arrayTableCompact, outdir = outdir) 2: >>>>>>>> aqm.writereport(modules = m, arrayTable = x$pData, >>>>>>>> reporttitle = reporttitle, outdir = outdir) 1: >>>>>>>> arrayQualityMetrics(rawAffyData, outdir = "quality", force = >>>>>>>> T) >>>>>>>> >>>>>>>> >>>>>>>> I guess this is still related to Cairo's version. I will >>>>>>>> probably try to use another version of Linux in another >>>>>>>> machine. >>>>>>>> >>>>>>>> Thanks again. If I have any comments or ideas for the >>>>>>>> package, I let you know. >>>>>>>> >>>>>>>> Cheers Paulo >>>>>>>> >>>>>>>> On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote: >>>>>>>> >>>>>>>>> Paulo >>>>>>>>> >>>>>>>>> what happens if you type >>>>>>>>> >>>>>>>>> system("xclock&") >>>>>>>>> >>>>>>>>> (Or, in the Unix shell, simply "xclock&"). Do you see a >>>>>>>>> clock? >>>>>>>>> >>>>>>>>> One possible explanation, if you are logging into a server >>>>>>>>> remotely, that you have not enable X11 forwarding. >>>>>>>>> >>>>>>>>> Why R's png() device needs an X11 server is a different >>>>>>>>> story... >>>>>>>>> >>>>>>>>> Best wishes Wolfgang >>>>>>>>> >>>>>>>>> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto: >>>>>>>>>> Hi Wolfgang >>>>>>>>>> >>>>>>>>>> Thanks a lot for your message. I was able to install this >>>>>>>>>> version, both on a release version and on a devel version >>>>>>>>>> of R, but I'm running into an error again: >>>>>>>>>> >>>>>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", >>>>>>>>>>> force=T) >>>>>>>>>> The report will be written into directory 'quality'. >>>>>>>>>> Error in X11(paste("png::", filename, sep = ""), width, >>>>>>>>>> height, pointsize, : unable to start device PNG In >>>>>>>>>> addition: Warning message: In png(file = nameimg, h = h * >>>>>>>>>> dpi, w = w * dpi) : unable to open connection to X11 >>>>>>>>>> display '' >>>>>>>>>> >>>>>>>>>> Here are the capabilities >>>>>>>>>> >>>>>>>>>>> capabilities() >>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>> FALSE FALSE TRUE TRUE libxml fifo cledit >>>>>>>>>> iconv NLS profmem cairo TRUE TRUE TRUE >>>>>>>>>> TRUE TRUE FALSE TRUE >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Both versions are the same. I don't know if the error is >>>>>>>>>> due to X11 being FALSE. I don't understand why X11 is >>>>>>>>>> showing as FALSE, as the binaries were compiled with the >>>>>>>>>> --with-x flag, and at the end of configure we got >>>>>>>>>> >>>>>>>>>> Interfaces supported: X11 External libraries: >>>>>>>>>> readline Additional capabilities: PNG, JPEG, TIFF, NLS, >>>>>>>>>> cairo Options enabled: shared BLAS, R >>>>>>>>>> profiling >>>>>>>>>> >>>>>>>>>> All X11 (xorg-devel) libraries are installed. >>>>>>>>>> >>>>>>>>>> Thanks again for the help. >>>>>>>>>> >>>>>>>>>> Cheers Paulo >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote: >>>>>>>>>> >>>>>>>>>>> Dear Paulo >>>>>>>>>>> >>>>>>>>>>> there have been many improvements on the package since >>>>>>>>>>> the last release, and I would recommend trying the >>>>>>>>>>> devel version>=3.4.8 >>>>>>>>>>> >>>>>>>>>>> http://bioconductor.org/help/bioc- views/2.8/bioc/html/arrayQualityMetrics.html >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem. >>>>>>>>>>> >>>>>>>>>>> The package is in a state of beta-testing, with - the >>>>>>>>>>> presentation of the outlier detection in the reports >>>>>>>>>>> not yet fully cooked, - and I am not yet sure whether& >>>>>>>>>>> how well it works on 64bit Windows. >>>>>>>>>>> >>>>>>>>>>> I hope to finalise this within a week or three; any >>>>>>>>>>> user experiences and comments are welcome. >>>>>>>>>>> >>>>>>>>>>> A sneal preview of the new reports is here [2]. >>>>>>>>>>> >>>>>>>>>>> Wolfgang >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> [1] >>>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/attachments/20 110128/ca068c82/attachment.pl >>>>>>>>>>> >>>>>>>>>>> >>> [2] http://www- huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Paulo Nuin scripsit 10/02/11 02:10: >>>>>>>>>>>> Hi James >>>>>>>>>>>> >>>>>>>>>>>> I checked our Cairo version, and it seems quite old. >>>>>>>>>>>> I'm checking the best way to update, as we are using >>>>>>>>>>>> CentOS official package. If the problem persists >>>>>>>>>>>> after upgrade, I will report to the list. >>>>>>>>>>>> >>>>>>>>>>>> Thanks a lot for your help. >>>>>>>>>>>> >>>>>>>>>>>> Paulo >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Paulo, >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote: >>>>>>>>>>>>>> Hi everyone >>>>>>>>>>>>>> >>>>>>>>>>>>>> We just got a new HPC system to speed up our >>>>>>>>>>>>>> analysis, but we are having some problems with >>>>>>>>>>>>>> the end part of a arrayQualityMetrics run. >>>>>>>>>>>>>> >>>>>>>>>>>>>> It goes fine until section 5, were it is >>>>>>>>>>>>>> interrupted by an error >>>>>>>>>>>>>> >>>>>>>>>>>>>>> arrayQualityMetrics(rawAffyData, >>>>>>>>>>>>>>> outdir="quality", force=T) >>>>>>>>>>>>>> The report will be written into directory >>>>>>>>>>>>>> 'quality'. [[1]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> [[2]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> [[3]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> [[4]] >>>>>>>>>>>>>> >>>>>>>>>>>>>> Error in UseMethod("xmlAttrs", node) : no >>>>>>>>>>>>>> applicable method for 'xmlAttrs' applied to an >>>>>>>>>>>>>> object of class "NULL" In addition: There were 39 >>>>>>>>>>>>>> warnings (use warnings() to see them) >>>>>>>>>>>>> >>>>>>>>>>>>> The same happened on my system, the problem was a >>>>>>>>>>>>> very old version of cairo, see this thread: >>>>>>>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html >>>>>>>>>>>>> >>>>>>>>>>>>> >>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not. >>>>>>>>>>>>> >>>>>>>>>>>>> HTH, James. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Our sessionInfo and capabilities are below. R is >>>>>>>>>>>>>> compiled natively and most of the required >>>>>>>>>>>>>> libraries are present and compiled with the >>>>>>>>>>>>>> system. Any help is appreciated. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Cheers Paulo >>>>>>>>>>>>>> >>>>>>>>>>>>>>> capabilities() >>>>>>>>>>>>>> jpeg png tiff tcltk X11 aqua >>>>>>>>>>>>>> http/ftp sockets TRUE TRUE TRUE FALSE >>>>>>>>>>>>>> TRUE FALSE TRUE TRUE libxml fifo >>>>>>>>>>>>>> cledit iconv NLS profmem cairo TRUE >>>>>>>>>>>>>> TRUE TRUE TRUE TRUE FALSE >>>>>>>>>>>>>> TRUE >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> sessionInfo() >>>>>>>>>>>>>> R version 2.12.1 (2010-12-16) Platform: >>>>>>>>>>>>>> x86_64-unknown-linux-gnu (64-bit) >>>>>>>>>>>>>> >>>>>>>>>>>>>> locale: [1] LC_CTYPE=en_US.UTF-8 >>>>>>>>>>>>>> LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 >>>>>>>>>>>>>> LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C >>>>>>>>>>>>>> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 >>>>>>>>>>>>>> LC_NAME=C [9] LC_ADDRESS=C >>>>>>>>>>>>>> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >>>>>>>>>>>>>> LC_IDENTIFICATION=C >>>>>>>>>>>>>> >>>>>>>>>>>>>> attached base packages: [1] stats graphics >>>>>>>>>>>>>> grDevices utils datasets methods base >>>>>>>>>>>>>> >>>>>>>>>>>>>> other attached packages: [1] hgu133plus2cdf_2.7.0 >>>>>>>>>>>>>> arrayQualityMetrics_3.2.4 [3] vsn_3.18.0 >>>>>>>>>>>>>> affyPLM_1.26.0 [5] preprocessCore_1.12.0 >>>>>>>>>>>>>> gcrma_2.22.0 [7] affy_1.28.0 >>>>>>>>>>>>>> Biobase_2.10.0 >>>>>>>>>>>>>> >>>>>>>>>>>>>> loaded via a namespace (and not attached): [1] >>>>>>>>>>>>>> affyio_1.18.0 annotate_1.28.0 >>>>>>>>>>>>>> AnnotationDbi_1.12.0 [4] beadarray_2.0.3 >>>>>>>>>>>>>> Biostrings_2.18.2 DBI_0.2-5 [7] >>>>>>>>>>>>>> genefilter_1.32.0 grid_2.12.1 >>>>>>>>>>>>>> hwriter_1.3 [10] IRanges_1.8.8 >>>>>>>>>>>>>> KernSmooth_2.23-4 lattice_0.19-13 [13] >>>>>>>>>>>>>> latticeExtra_0.6-14 limma_3.6.9 >>>>>>>>>>>>>> marray_1.28.0 [16] RColorBrewer_1.0-2 >>>>>>>>>>>>>> RSQLite_0.9-4 simpleaffy_2.26.1 [19] >>>>>>>>>>>>>> splines_2.12.1 stats4_2.12.1 >>>>>>>>>>>>>> survival_2.36-2 [22] SVGAnnotation_0.7-2 >>>>>>>>>>>>>> tools_2.12.1 XML_3.2-0 [25] xtable_1.5-6 >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> 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 >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> 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 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> >>> -- >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Wolfgang Huber EMBL >>>>>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>>> >>> -- >>>>>>>>> >>>>>>>>> >>>>>>>>> Wolfgang Huber EMBL >>>>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> >>>>>>> Wolfgang Huber EMBL >>>>>>> http://www.embl.de/research/units/genome_biology/huber >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> Wolfgang Huber EMBL >>>>> http://www.embl.de/research/units/genome_biology/huber >>>>> >>>>> >>>> >>> >>> -- >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >