arrayQualityMetrics
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@guillaume-meurice-4494
Last seen 10.2 years ago
Dear All, I have a problem with arrayQualityMetrics (see following code). I would be very grateful if you could provide me with any idea so I can fixe the problem. Thanks you by advance. R code that produce the problem : #################################################################### > a = sessionInfo() > arrayQualityMetrics(eSet, outdir="aqmRaw", do.logtransform=T) The directory 'aqmRaw' has been created. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] libpng warning: Application was compiled with png.h from libpng-1.2.26 libpng warning: Application is running with png.c from libpng-1.4.1 libpng warning: Incompatible libpng version in application and library libpng warning: Application was compiled with png.h from libpng-1.2.26 libpng warning: Application is running with png.c from libpng-1.4.1 libpng warning: Incompatible libpng version in application and library Error in svg(file = svgtemp, h = h, w = w) : cairo-based devices are not supported on this build > > b = sessionInfo() > #################################################################### Difference between 'a' and 'b' sessionInfo #################################################################### > summary(a) Length Class Mode R.version 13 -none- list platform 1 -none- character locale 1 -none- character basePkgs 7 -none- character otherPkgs 7 -none- list loadedOnly 23 -none- list > summary(b) Length Class Mode R.version 13 -none- list platform 1 -none- character locale 1 -none- character basePkgs 7 -none- character otherPkgs 7 -none- list loadedOnly 24 -none- list > #################################################################### the 'a' sessionInfo #################################################################### R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 [6] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 RColorBrewer_1.0-2 RSQLite_0.9-4 [7] SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 genefilter_1.32.0 [13] grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 [19] simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 the 'b' sessionInfo #################################################################### > b R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 [6] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 KernSmooth_2.23-4 RColorBrewer_1.0-2 [7] RSQLite_0.9-4 SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 [13] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 [19] marray_1.28.0 simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 > -- Guillaume [[alternative HTML version deleted]]
arrayQualityMetrics arrayQualityMetrics • 2.4k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Guillaume it looks like your R installation is broken (the warning about libpng) and lacks the 'svg' device. Can you please try with installing R 2.13 (i.e. currently a prelease 'beta' version) and the current version of arrayQualityMetrics (http://www.bioconductor.org/help/bioc- views/devel/bioc/html/arrayQualityMetrics.html), which has greatly changed over that from the last release. Best wishes Wolfgang Il Apr/1/11 9:14 AM, Guillaume Meurice ha scritto: > Dear All, > > I have a problem with arrayQualityMetrics (see following code). > I would be very grateful if you could provide me with any idea so I can fixe the problem. > Thanks you by advance. > > > R code that produce the problem : > #################################################################### >> a = sessionInfo() >> arrayQualityMetrics(eSet, outdir="aqmRaw", do.logtransform=T) > The directory 'aqmRaw' has been created. > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > (loaded the KernSmooth namespace) > [[1]] > libpng warning: Application was compiled with png.h from libpng-1.2.26 > libpng warning: Application is running with png.c from libpng-1.4.1 > libpng warning: Incompatible libpng version in application and library > > libpng warning: Application was compiled with png.h from libpng-1.2.26 > libpng warning: Application is running with png.c from libpng-1.4.1 > libpng warning: Incompatible libpng version in application and library > Error in svg(file = svgtemp, h = h, w = w) : > cairo-based devices are not supported on this build > >> >> b = sessionInfo() >> > #################################################################### > > > Difference between 'a' and 'b' sessionInfo > #################################################################### >> summary(a) > Length Class Mode > R.version 13 -none- list > platform 1 -none- character > locale 1 -none- character > basePkgs 7 -none- character > otherPkgs 7 -none- list > loadedOnly 23 -none- list >> summary(b) > Length Class Mode > R.version 13 -none- list > platform 1 -none- character > locale 1 -none- character > basePkgs 7 -none- character > otherPkgs 7 -none- list > loadedOnly 24 -none- list >> > #################################################################### > > > > > the 'a' sessionInfo > #################################################################### > R version 2.12.2 (2011-02-25) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 > [6] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 RColorBrewer_1.0-2 RSQLite_0.9-4 > [7] SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 genefilter_1.32.0 > [13] grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 > [19] simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 > > > the 'b' sessionInfo > #################################################################### >> b > R version 2.12.2 (2011-02-25) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 > [6] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 KernSmooth_2.23-4 RColorBrewer_1.0-2 > [7] RSQLite_0.9-4 SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 > [13] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 > [19] marray_1.28.0 simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >> > > > > -- > Guillaume > > > [[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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Wolfgang, thanks for your answer. Unfortunately, I was not able to install the R.2.13 beta release (compilation won't work know). I will have to wait for the stable release that seems to come up to the 13th of April (or I hope so). Best regards, -- Guillaume Meurice - PhD Bioinformaticien Unit? de G?nomique Fonctionnelle PR2 - Bureau 323.2 Poste : 3509 Institut Gustave Roussy - PR2 114 rue Edouard Vaillant - 94805 VILLEJUIF Cedex tel : +33 (0)1 42 11 42 11 (poste 3509) fax : +33 (0)1 42 11 62 67 Le Apr 1, 2011 ? 11:21 PM, Wolfgang Huber a ?crit : > Dear Guillaume > > it looks like your R installation is broken (the warning about libpng) and lacks the 'svg' device. > > Can you please try with installing R 2.13 (i.e. currently a prelease 'beta' version) and the current version of arrayQualityMetrics (http://www.bioconductor.org/help/bioc- views/devel/bioc/html/arrayQualityMetrics.html), which has greatly changed over that from the last release. > > Best wishes > Wolfgang > > > > Il Apr/1/11 9:14 AM, Guillaume Meurice ha scritto: >> Dear All, >> >> I have a problem with arrayQualityMetrics (see following code). >> I would be very grateful if you could provide me with any idea so I can fixe the problem. >> Thanks you by advance. >> >> >> R code that produce the problem : >> #################################################################### >>> a = sessionInfo() >>> arrayQualityMetrics(eSet, outdir="aqmRaw", do.logtransform=T) >> The directory 'aqmRaw' has been created. >> KernSmooth 2.23 loaded >> Copyright M. P. Wand 1997-2009 >> (loaded the KernSmooth namespace) >> [[1]] >> libpng warning: Application was compiled with png.h from libpng-1.2.26 >> libpng warning: Application is running with png.c from libpng-1.4.1 >> libpng warning: Incompatible libpng version in application and library >> >> libpng warning: Application was compiled with png.h from libpng-1.2.26 >> libpng warning: Application is running with png.c from libpng-1.4.1 >> libpng warning: Incompatible libpng version in application and library >> Error in svg(file = svgtemp, h = h, w = w) : >> cairo-based devices are not supported on this build >> >>> >>> b = sessionInfo() >>> >> #################################################################### >> >> >> Difference between 'a' and 'b' sessionInfo >> #################################################################### >>> summary(a) >> Length Class Mode >> R.version 13 -none- list >> platform 1 -none- character >> locale 1 -none- character >> basePkgs 7 -none- character >> otherPkgs 7 -none- list >> loadedOnly 23 -none- list >>> summary(b) >> Length Class Mode >> R.version 13 -none- list >> platform 1 -none- character >> locale 1 -none- character >> basePkgs 7 -none- character >> otherPkgs 7 -none- list >> loadedOnly 24 -none- list >>> >> #################################################################### >> >> >> >> >> the 'a' sessionInfo >> #################################################################### >> R version 2.12.2 (2011-02-25) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 >> [6] affy_1.28.0 Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 RColorBrewer_1.0-2 RSQLite_0.9-4 >> [7] SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 genefilter_1.32.0 >> [13] grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >> [19] simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >> >> >> the 'b' sessionInfo >> #################################################################### >>> b >> R version 2.12.2 (2011-02-25) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 >> [6] affy_1.28.0 Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 KernSmooth_2.23-4 RColorBrewer_1.0-2 >> [7] RSQLite_0.9-4 SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 >> [13] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 >> [19] marray_1.28.0 simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >>> >> >> >> >> -- >> Guillaume >> >> >> [[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 > > -- > > > 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
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Dear Guillaume it is likely that your compilation problem is not related to whether you use a current R-beta or you wait till 13th, i.e. it might just as well be worthwhile to solve it now. You could post a more precise description of your compilation problem here, or perhaps more appropriate, R-help. Best wishes Wolfgang. Guillaume Meurice scripsit 04/04/11 09:11: > Dear Wolfgang, > > thanks for your answer. > > Unfortunately, I was not able to install the R.2.13 beta release (compilation won't work know). I will have to wait for the stable release that seems to come up to the 13th of April (or I hope so). > > > > Best regards, > -- > Guillaume Meurice - PhD > Bioinformaticien > > Unit? de G?nomique Fonctionnelle > > PR2 - Bureau 323.2 > Poste : 3509 > > Institut Gustave Roussy - PR2 > 114 rue Edouard Vaillant - 94805 VILLEJUIF Cedex > tel : +33 (0)1 42 11 42 11 (poste 3509) > fax : +33 (0)1 42 11 62 67 > > Le Apr 1, 2011 ? 11:21 PM, Wolfgang Huber a ?crit : > >> Dear Guillaume >> >> it looks like your R installation is broken (the warning about libpng) and lacks the 'svg' device. >> >> Can you please try with installing R 2.13 (i.e. currently a prelease 'beta' version) and the current version of arrayQualityMetrics (http://www.bioconductor.org/help/bioc- views/devel/bioc/html/arrayQualityMetrics.html), which has greatly changed over that from the last release. >> >> Best wishes >> Wolfgang >> >> >> >> Il Apr/1/11 9:14 AM, Guillaume Meurice ha scritto: >>> Dear All, >>> >>> I have a problem with arrayQualityMetrics (see following code). >>> I would be very grateful if you could provide me with any idea so I can fixe the problem. >>> Thanks you by advance. >>> >>> >>> R code that produce the problem : >>> #################################################################### >>>> a = sessionInfo() >>>> arrayQualityMetrics(eSet, outdir="aqmRaw", do.logtransform=T) >>> The directory 'aqmRaw' has been created. >>> KernSmooth 2.23 loaded >>> Copyright M. P. Wand 1997-2009 >>> (loaded the KernSmooth namespace) >>> [[1]] >>> libpng warning: Application was compiled with png.h from libpng-1.2.26 >>> libpng warning: Application is running with png.c from libpng-1.4.1 >>> libpng warning: Incompatible libpng version in application and library >>> >>> libpng warning: Application was compiled with png.h from libpng-1.2.26 >>> libpng warning: Application is running with png.c from libpng-1.4.1 >>> libpng warning: Incompatible libpng version in application and library >>> Error in svg(file = svgtemp, h = h, w = w) : >>> cairo-based devices are not supported on this build >>> >>>> >>>> b = sessionInfo() >>>> >>> #################################################################### >>> >>> >>> Difference between 'a' and 'b' sessionInfo >>> #################################################################### >>>> summary(a) >>> Length Class Mode >>> R.version 13 -none- list >>> platform 1 -none- character >>> locale 1 -none- character >>> basePkgs 7 -none- character >>> otherPkgs 7 -none- list >>> loadedOnly 23 -none- list >>>> summary(b) >>> Length Class Mode >>> R.version 13 -none- list >>> platform 1 -none- character >>> locale 1 -none- character >>> basePkgs 7 -none- character >>> otherPkgs 7 -none- list >>> loadedOnly 24 -none- list >>>> >>> #################################################################### >>> >>> >>> >>> >>> the 'a' sessionInfo >>> #################################################################### >>> R version 2.12.2 (2011-02-25) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 >>> [6] affy_1.28.0 Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 RColorBrewer_1.0-2 RSQLite_0.9-4 >>> [7] SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 genefilter_1.32.0 >>> [13] grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>> [19] simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >>> >>> >>> the 'b' sessionInfo >>> #################################################################### >>>> b >>> R version 2.12.2 (2011-02-25) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 >>> [6] affy_1.28.0 Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 KernSmooth_2.23-4 RColorBrewer_1.0-2 >>> [7] RSQLite_0.9-4 SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 >>> [13] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 >>> [19] marray_1.28.0 simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >>>> >>> >>> >>> >>> -- >>> Guillaume >>> >>> >>> [[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 >> >> -- >> >> >> 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
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Dear Wolfgang, Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. Regards, -- Guillaume Meurice - PhD Bioinformaticien > Dear Guillaume > > it is likely that your compilation problem is not related to whether you use a current R-beta or you wait till 13th, i.e. it might just as well be worthwhile to solve it now. > > You could post a more precise description of your compilation problem here, or perhaps more appropriate, R-help. > > Best wishes > Wolfgang. > > > > Guillaume Meurice scripsit 04/04/11 09:11: >> Dear Wolfgang, >> >> thanks for your answer. >> >> Unfortunately, I was not able to install the R.2.13 beta release (compilation won't work know). I will have to wait for the stable release that seems to come up to the 13th of April (or I hope so). >> >> >> >> Best regards, >> -- >> Guillaume Meurice - PhD >> Bioinformaticien >> >> Unit? de G?nomique Fonctionnelle >> >> PR2 - Bureau 323.2 >> Poste : 3509 >> >> Institut Gustave Roussy - PR2 >> 114 rue Edouard Vaillant - 94805 VILLEJUIF Cedex >> tel : +33 (0)1 42 11 42 11 (poste 3509) >> fax : +33 (0)1 42 11 62 67 >> >> Le Apr 1, 2011 ? 11:21 PM, Wolfgang Huber a ?crit : >> >>> Dear Guillaume >>> >>> it looks like your R installation is broken (the warning about libpng) and lacks the 'svg' device. >>> >>> Can you please try with installing R 2.13 (i.e. currently a prelease 'beta' version) and the current version of arrayQualityMetrics (http://www.bioconductor.org/help/bioc- views/devel/bioc/html/arrayQualityMetrics.html), which has greatly changed over that from the last release. >>> >>> Best wishes >>> Wolfgang >>> >>> >>> >>> Il Apr/1/11 9:14 AM, Guillaume Meurice ha scritto: >>>> Dear All, >>>> >>>> I have a problem with arrayQualityMetrics (see following code). >>>> I would be very grateful if you could provide me with any idea so I can fixe the problem. >>>> Thanks you by advance. >>>> >>>> >>>> R code that produce the problem : >>>> #################################################################### >>>>> a = sessionInfo() >>>>> arrayQualityMetrics(eSet, outdir="aqmRaw", do.logtransform=T) >>>> The directory 'aqmRaw' has been created. >>>> KernSmooth 2.23 loaded >>>> Copyright M. P. Wand 1997-2009 >>>> (loaded the KernSmooth namespace) >>>> [[1]] >>>> libpng warning: Application was compiled with png.h from libpng-1.2.26 >>>> libpng warning: Application is running with png.c from libpng-1.4.1 >>>> libpng warning: Incompatible libpng version in application and library >>>> >>>> libpng warning: Application was compiled with png.h from libpng-1.2.26 >>>> libpng warning: Application is running with png.c from libpng-1.4.1 >>>> libpng warning: Incompatible libpng version in application and library >>>> Error in svg(file = svgtemp, h = h, w = w) : >>>> cairo-based devices are not supported on this build >>>> >>>>> >>>>> b = sessionInfo() >>>>> >>>> #################################################################### >>>> >>>> >>>> Difference between 'a' and 'b' sessionInfo >>>> #################################################################### >>>>> summary(a) >>>> Length Class Mode >>>> R.version 13 -none- list >>>> platform 1 -none- character >>>> locale 1 -none- character >>>> basePkgs 7 -none- character >>>> otherPkgs 7 -none- list >>>> loadedOnly 23 -none- list >>>>> summary(b) >>>> Length Class Mode >>>> R.version 13 -none- list >>>> platform 1 -none- character >>>> locale 1 -none- character >>>> basePkgs 7 -none- character >>>> otherPkgs 7 -none- list >>>> loadedOnly 24 -none- list >>>>> >>>> #################################################################### >>>> >>>> >>>> >>>> >>>> the 'a' sessionInfo >>>> #################################################################### >>>> R version 2.12.2 (2011-02-25) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 >>>> [6] affy_1.28.0 Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 RColorBrewer_1.0-2 RSQLite_0.9-4 >>>> [7] SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 genefilter_1.32.0 >>>> [13] grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0 >>>> [19] simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >>>> >>>> >>>> the 'b' sessionInfo >>>> #################################################################### >>>>> b >>>> R version 2.12.2 (2011-02-25) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 >>>> [6] affy_1.28.0 Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 IRanges_1.8.8 KernSmooth_2.23-4 RColorBrewer_1.0-2 >>>> [7] RSQLite_0.9-4 SVGAnnotation_0.7-2 XML_3.2-0 affyio_1.18.0 annotate_1.28.0 beadarray_2.0.3 >>>> [13] genefilter_1.32.0 grid_2.12.2 hwriter_1.3 lattice_0.19-17 latticeExtra_0.6-14 limma_3.6.9 >>>> [19] marray_1.28.0 simpleaffy_2.26.1 splines_2.12.2 stats4_2.12.2 survival_2.36-5 xtable_1.5-6 >>>>> >>>> >>>> >>>> >>>> -- >>>> Guillaume >>>> >>>> >>>> [[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 >>> >>> -- >>> >>> >>> 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 > >
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Hi Guillaume, On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice <guillaume.meurice at="" igr.fr=""> wrote: > Dear Wolfgang, > > Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. > > But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. If you find that you'd rather use the R.app GUI with R-2.13, you can grab it from here: http://r.research.att.com/#GUI Go to the select the one that's appropriate for your architecture. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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How nice ! thanks you for the tricks. -- Guillaume Meurice - PhD Bioinformaticien Le Apr 4, 2011 ? 4:09 PM, Steve Lianoglou a ?crit : > Hi Guillaume, > > On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice > <guillaume.meurice at="" igr.fr=""> wrote: >> Dear Wolfgang, >> >> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >> >> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. > > If you find that you'd rather use the R.app GUI with R-2.13, you can > grab it from here: > > http://r.research.att.com/#GUI > > Go to the select the one that's appropriate for your architecture. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact
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Dear Wolgang, Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: ======================================= source("http://www.bioconductor.org/biocLite.R") biocLite("arrayQualityMetrics") Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. Installing Bioconductor version 2.8 packages: [1] "arrayQualityMetrics" Please wait... also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' ======================================= it fails, raising the following error: ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' Best regards, -- Guillaume Meurice - PhD Bioinformaticien Le Apr 4, 2011 ? 4:41 PM, Guillaume Meurice a ?crit : > How nice ! thanks you for the tricks. > > -- > Guillaume Meurice - PhD > Bioinformaticien > Le Apr 4, 2011 ? 4:09 PM, Steve Lianoglou a ?crit : > >> Hi Guillaume, >> >> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >> <guillaume.meurice at="" igr.fr=""> wrote: >>> Dear Wolfgang, >>> >>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>> >>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >> >> If you find that you'd rather use the R.app GUI with R-2.13, you can >> grab it from here: >> >> http://r.research.att.com/#GUI >> >> Go to the select the one that's appropriate for your architecture. >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > 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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Hi Guillame, what happens when you do this: source("http://www.bioconductor.org/biocLite.R") biocLite('Cairo') biocLite("SVGAnnotation") Mark On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: > Dear Wolgang, > > Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: > ======================================= > source("http://www.bioconductor.org/biocLite.R") > biocLite("arrayQualityMetrics") > > Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. > Installing Bioconductor version 2.8 packages: > [1] "arrayQualityMetrics" > Please wait... > > also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' > ======================================= > > it fails, raising the following error: > > ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' > > > Best regards, > -- > Guillaume Meurice - PhD > Bioinformaticien > > > > Le Apr 4, 2011 à 4:41 PM, Guillaume Meurice a écrit : > >> How nice ! thanks you for the tricks. >> >> -- >> Guillaume Meurice - PhD >> Bioinformaticien >> Le Apr 4, 2011 à 4:09 PM, Steve Lianoglou a écrit : >> >>> Hi Guillaume, >>> >>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>> <guillaume.meurice@igr.fr> wrote: >>>> Dear Wolfgang, >>>> >>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>> >>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>> >>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>> grab it from here: >>> >>> http://r.research.att.com/#GUI >>> >>> Go to the select the one that's appropriate for your architecture. >>> >>> -steve >>> >>> -- >>> Steve Lianoglou >>> Graduate Student: Computational Systems Biology >>> | Memorial Sloan-Kettering Cancer Center >>> | Weill Medical College of Cornell University >>> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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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Hi Mark When trying to install separatly Cairo and SVGAnnotation, I got the following error message : ###################################################################### ############ source("http://www.bioconductor.org/biocLite.R") biocLite('Cairo') Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. Installing Bioconductor version 2.8 packages: [1] "Cairo" Please wait... trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz' Content type 'application/x-gzip' length 78688 bytes (76 Kb) opened URL ================================================== downloaded 76 Kb configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. ERROR: configuration failed for package 'Cairo' * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/li brary/Cairo' ###################################################################### ############ and for SVGAnnotation (that seems to need Cairo to be installed) ###################################################################### ############ source("http://www.bioconductor.org/biocLite.R") biocLite("SVGAnnotation") Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. Installing Bioconductor version 2.8 packages: [1] "SVGAnnotation" Please wait... trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/contrib /SVGAnnotation_0.9-0.tar.gz' Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb) opened URL ================================================== downloaded 4.5 Mb During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" * installing *source* package 'SVGAnnotation' ... > q(status = capabilities()["cairo"] == FALSE) ***** Using the Cairo package. configure: creating ./config.status config.status: creating DESCRIPTION config.status: creating R/config.R ** R ** data ** inst ** preparing package for lazy loading Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'Cairo' Error : package 'Cairo' could not be loaded ERROR: lazy loading failed for package 'SVGAnnotation' * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/li brary/SVGAnnotation' ###################################################################### ############ Best regards, -- Guillaume Meurice - PhD Bioinformaticien Le Apr 5, 2011 à 2:22 AM, Mark Cowley a écrit : > Hi Guillame, > what happens when you do this: > source("http://www.bioconductor.org/biocLite.R") > biocLite('Cairo') > biocLite("SVGAnnotation") > > Mark > > On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: > >> Dear Wolgang, >> >> Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: >> ======================================= >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("arrayQualityMetrics") >> >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "arrayQualityMetrics" >> Please wait... >> >> also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' >> ======================================= >> >> it fails, raising the following error: >> >> ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' >> >> >> Best regards, >> -- >> Guillaume Meurice - PhD >> Bioinformaticien >> >> >> >> Le Apr 4, 2011 à 4:41 PM, Guillaume Meurice a écrit : >> >>> How nice ! thanks you for the tricks. >>> >>> -- >>> Guillaume Meurice - PhD >>> Bioinformaticien >>> Le Apr 4, 2011 à 4:09 PM, Steve Lianoglou a écrit : >>> >>>> Hi Guillaume, >>>> >>>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>>> <guillaume.meurice@igr.fr> wrote: >>>>> Dear Wolfgang, >>>>> >>>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>>> >>>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>>> >>>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>>> grab it from here: >>>> >>>> http://r.research.att.com/#GUI >>>> >>>> Go to the select the one that's appropriate for your architecture. >>>> >>>> -steve >>>> >>>> -- >>>> Steve Lianoglou >>>> Graduate Student: Computational Systems Biology >>>> | Memorial Sloan-Kettering Cancer Center >>>> | Weill Medical College of Cornell University >>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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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Dear Guillaume you're right, the Cairo package is the hard part, SVGAnnotation should install without further ado once you have Cairo. The error message that you have got is pretty explicit. There are two ways to install R packages: from source, or precompiled binary versions. 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' www.macports.org) for that. 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html . As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation. Hope this helps Wolfgang Guillaume Meurice scripsit 05/04/11 08:03: > Hi Mark > > When trying to install separatly Cairo and SVGAnnotation, I got the following error message : > > #################################################################### ############## > source("http://www.bioconductor.org/biocLite.R") > biocLite('Cairo') > Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. > Installing Bioconductor version 2.8 packages: > [1] "Cairo" > Please wait... > > trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz' > Content type 'application/x-gzip' length 78688 bytes (76 Kb) > opened URL > ================================================== > downloaded 76 Kb > > configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. > ERROR: configuration failed for package 'Cairo' > * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/Cairo' > > #################################################################### ############## > > > > and for SVGAnnotation (that seems to need Cairo to be installed) > > #################################################################### ############## > source("http://www.bioconductor.org/biocLite.R") > biocLite("SVGAnnotation") > Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. > Installing Bioconductor version 2.8 packages: > [1] "SVGAnnotation" > Please wait... > > trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/contr ib/SVGAnnotation_0.9-0.tar.gz' > Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb) > opened URL > ================================================== > downloaded 4.5 Mb > > During startup - Warning messages: > 1: Setting LC_CTYPE failed, using "C" > 2: Setting LC_TIME failed, using "C" > 3: Setting LC_MESSAGES failed, using "C" > * installing *source* package 'SVGAnnotation' ... >> q(status = capabilities()["cairo"] == FALSE) > ***** Using the Cairo package. > configure: creating ./config.status > config.status: creating DESCRIPTION > config.status: creating R/config.R > ** R > ** data > ** inst > ** preparing package for lazy loading > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : > there is no package called 'Cairo' > Error : package 'Cairo' could not be loaded > ERROR: lazy loading failed for package 'SVGAnnotation' > * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/SVGAnnotation' > #################################################################### ############## > > > > > Best regards, > -- > Guillaume Meurice - PhD > Bioinformaticien > > Le Apr 5, 2011 ? 2:22 AM, Mark Cowley a ?crit : > >> Hi Guillame, >> what happens when you do this: >> source("http://www.bioconductor.org/biocLite.R") >> biocLite('Cairo') >> biocLite("SVGAnnotation") >> >> Mark >> >> On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: >> >>> Dear Wolgang, >>> >>> Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: >>> ======================================= >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("arrayQualityMetrics") >>> >>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>> Installing Bioconductor version 2.8 packages: >>> [1] "arrayQualityMetrics" >>> Please wait... >>> >>> also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' >>> ======================================= >>> >>> it fails, raising the following error: >>> >>> ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' >>> >>> >>> Best regards, >>> -- >>> Guillaume Meurice - PhD >>> Bioinformaticien >>> >>> >>> >>> Le Apr 4, 2011 ? 4:41 PM, Guillaume Meurice a ?crit : >>> >>>> How nice ! thanks you for the tricks. >>>> >>>> -- >>>> Guillaume Meurice - PhD >>>> Bioinformaticien >>>> Le Apr 4, 2011 ? 4:09 PM, Steve Lianoglou a ?crit : >>>> >>>>> Hi Guillaume, >>>>> >>>>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>>>> <guillaume.meurice at="" igr.fr=""> wrote: >>>>>> Dear Wolfgang, >>>>>> >>>>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>>>> >>>>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>>>> >>>>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>>>> grab it from here: >>>>> >>>>> http://r.research.att.com/#GUI >>>>> >>>>> Go to the select the one that's appropriate for your architecture. >>>>> >>>>> -steve >>>>> >>>>> -- >>>>> Steve Lianoglou >>>>> Graduate Student: Computational Systems Biology >>>>> | Memorial Sloan-Kettering Cancer Center >>>>> | Weill Medical College of Cornell University >>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>> >>>> _______________________________________________ >>>> 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 >> > > > [[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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Wolfgang, > 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' www.macports.org) for that. After installing mac ports, I wasn't able to sync and selfupdate it, probably because I'm behind a very restricitive proxy at my work .... so I can't properly install cairo system library by this way. > 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html . > As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation. In this case, I was not able to install "Cairo" R package, the error message was the following : ###################################################################### #### configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. ERROR: configuration failed for package 'Cairo' * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/li brary/Cairo' ###################################################################### #### I'll try to contact Simon Urbanek on R-SIG-MAC mailing list. Regards, -- Guillaume Meurice - PhD Bioinformaticien > > Dear Guillaume > > you're right, the Cairo package is the hard part, SVGAnnotation should install without further ado once you have Cairo. The error message that you have got is pretty explicit. > > There are two ways to install R packages: from source, or precompiled binary versions. > > 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' www.macports.org) for that. > > 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html . > As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation. > > Hope this helps > Wolfgang > > > Guillaume Meurice scripsit 05/04/11 08:03: >> Hi Mark >> >> When trying to install separatly Cairo and SVGAnnotation, I got the following error message : >> >> ################################################################### ############### >> source("http://www.bioconductor.org/biocLite.R") >> biocLite('Cairo') >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "Cairo" >> Please wait... >> >> trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz' >> Content type 'application/x-gzip' length 78688 bytes (76 Kb) >> opened URL >> ================================================== >> downloaded 76 Kb >> >> configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. >> ERROR: configuration failed for package 'Cairo' >> * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources /library/Cairo' >> >> ################################################################### ############### >> >> >> >> and for SVGAnnotation (that seems to need Cairo to be installed) >> >> ################################################################### ############### >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("SVGAnnotation") >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "SVGAnnotation" >> Please wait... >> >> trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/cont rib/SVGAnnotation_0.9-0.tar.gz' >> Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb) >> opened URL >> ================================================== >> downloaded 4.5 Mb >> >> During startup - Warning messages: >> 1: Setting LC_CTYPE failed, using "C" >> 2: Setting LC_TIME failed, using "C" >> 3: Setting LC_MESSAGES failed, using "C" >> * installing *source* package 'SVGAnnotation' ... >>> q(status = capabilities()["cairo"] == FALSE) >> ***** Using the Cairo package. >> configure: creating ./config.status >> config.status: creating DESCRIPTION >> config.status: creating R/config.R >> ** R >> ** data >> ** inst >> ** preparing package for lazy loading >> Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : >> there is no package called 'Cairo' >> Error : package 'Cairo' could not be loaded >> ERROR: lazy loading failed for package 'SVGAnnotation' >> * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources /library/SVGAnnotation' >> ################################################################### ############### >> >> >> >> >> Best regards, >> -- >> Guillaume Meurice - PhD >> Bioinformaticien >> >> Le Apr 5, 2011 à 2:22 AM, Mark Cowley a écrit : >> >>> Hi Guillame, >>> what happens when you do this: >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite('Cairo') >>> biocLite("SVGAnnotation") >>> >>> Mark >>> >>> On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: >>> >>>> Dear Wolgang, >>>> >>>> Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: >>>> ======================================= >>>> source("http://www.bioconductor.org/biocLite.R") >>>> biocLite("arrayQualityMetrics") >>>> >>>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>>> Installing Bioconductor version 2.8 packages: >>>> [1] "arrayQualityMetrics" >>>> Please wait... >>>> >>>> also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' >>>> ======================================= >>>> >>>> it fails, raising the following error: >>>> >>>> ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' >>>> >>>> >>>> Best regards, >>>> -- >>>> Guillaume Meurice - PhD >>>> Bioinformaticien >>>> >>>> >>>> >>>> Le Apr 4, 2011 à 4:41 PM, Guillaume Meurice a écrit : >>>> >>>>> How nice ! thanks you for the tricks. >>>>> >>>>> -- >>>>> Guillaume Meurice - PhD >>>>> Bioinformaticien >>>>> Le Apr 4, 2011 à 4:09 PM, Steve Lianoglou a écrit : >>>>> >>>>>> Hi Guillaume, >>>>>> >>>>>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>>>>> <guillaume.meurice@igr.fr> wrote: >>>>>>> Dear Wolfgang, >>>>>>> >>>>>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>>>>> >>>>>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>>>>> >>>>>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>>>>> grab it from here: >>>>>> >>>>>> http://r.research.att.com/#GUI >>>>>> >>>>>> Go to the select the one that's appropriate for your architecture. >>>>>> >>>>>> -steve >>>>>> >>>>>> -- >>>>>> Steve Lianoglou >>>>>> Graduate Student: Computational Systems Biology >>>>>> | Memorial Sloan-Kettering Cancer Center >>>>>> | Weill Medical College of Cornell University >>>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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]] >> >> >> >> >> _______________________________________________ >> 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 > > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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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>> 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html . >> As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation. > > In this case, I was not able to install "Cairo" R package, the error message was the following : > > #################################################################### ###### > configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. > ERROR: configuration failed for package 'Cairo' > * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/Cairo' ###################################################################### #### Here 's the answer from S. Urbanek about the installation of the R package "Cairo" for 64-bit build : """ Fair enough - the 64-bit iconv has different symbols than at the time ft was built so the 64-bit build fails. So for now you'll have to stick with R --arch i386 for the Cairo binary. In the meantime I'll see if I can build a fresh set of static ft that will work with the current iconv - it's a bit convoluted as we need a build that won't use CF so Cairo can be forked (for multicore, Rserve etc.). Cheers, Simon """ -- Guillaume Meurice - PhD Bioinformaticien Le Apr 5, 2011 ? 3:18 PM, Guillaume Meurice a ?crit : > Dear Wolfgang, > >> 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' www.macports.org) for that. > > After installing mac ports, I wasn't able to sync and selfupdate it, probably because I'm behind a very restricitive proxy at my work .... so I can't properly install cairo system library by this way. > > >> 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html . >> As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation. > > In this case, I was not able to install "Cairo" R package, the error message was the following : > > #################################################################### ###### > configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. > ERROR: configuration failed for package 'Cairo' > * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/Cairo' > #################################################################### ###### > > I'll try to contact Simon Urbanek on R-SIG-MAC mailing list. > > > Regards, > -- > Guillaume Meurice - PhD > Bioinformaticien > >> >> Dear Guillaume >> >> you're right, the Cairo package is the hard part, SVGAnnotation should install without further ado once you have Cairo. The error message that you have got is pretty explicit. >> >> There are two ways to install R packages: from source, or precompiled binary versions. >> >> 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' www.macports.org) for that. >> >> 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html . >> As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation. >> >> Hope this helps >> Wolfgang >> >> >> Guillaume Meurice scripsit 05/04/11 08:03: >>> Hi Mark >>> >>> When trying to install separatly Cairo and SVGAnnotation, I got the following error message : >>> >>> ################################################################## ################ >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite('Cairo') >>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>> Installing Bioconductor version 2.8 packages: >>> [1] "Cairo" >>> Please wait... >>> >>> trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz' >>> Content type 'application/x-gzip' length 78688 bytes (76 Kb) >>> opened URL >>> ================================================== >>> downloaded 76 Kb >>> >>> configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. >>> ERROR: configuration failed for package 'Cairo' >>> * removing '/Library/Frameworks/R.framework/Versions/2.13/Resource s/library/Cairo' >>> >>> ################################################################## ################ >>> >>> >>> >>> and for SVGAnnotation (that seems to need Cairo to be installed) >>> >>> ################################################################## ################ >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("SVGAnnotation") >>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>> Installing Bioconductor version 2.8 packages: >>> [1] "SVGAnnotation" >>> Please wait... >>> >>> trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/con trib/SVGAnnotation_0.9-0.tar.gz' >>> Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb) >>> opened URL >>> ================================================== >>> downloaded 4.5 Mb >>> >>> During startup - Warning messages: >>> 1: Setting LC_CTYPE failed, using "C" >>> 2: Setting LC_TIME failed, using "C" >>> 3: Setting LC_MESSAGES failed, using "C" >>> * installing *source* package 'SVGAnnotation' ... >>>> q(status = capabilities()["cairo"] == FALSE) >>> ***** Using the Cairo package. >>> configure: creating ./config.status >>> config.status: creating DESCRIPTION >>> config.status: creating R/config.R >>> ** R >>> ** data >>> ** inst >>> ** preparing package for lazy loading >>> Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : >>> there is no package called 'Cairo' >>> Error : package 'Cairo' could not be loaded >>> ERROR: lazy loading failed for package 'SVGAnnotation' >>> * removing '/Library/Frameworks/R.framework/Versions/2.13/Resource s/library/SVGAnnotation' >>> ################################################################## ################ >>> >>> >>> >>> >>> Best regards, >>> -- >>> Guillaume Meurice - PhD >>> Bioinformaticien >>> >>> Le Apr 5, 2011 ? 2:22 AM, Mark Cowley a ?crit : >>> >>>> Hi Guillame, >>>> what happens when you do this: >>>> source("http://www.bioconductor.org/biocLite.R") >>>> biocLite('Cairo') >>>> biocLite("SVGAnnotation") >>>> >>>> Mark >>>> >>>> On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: >>>> >>>>> Dear Wolgang, >>>>> >>>>> Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: >>>>> ======================================= >>>>> source("http://www.bioconductor.org/biocLite.R") >>>>> biocLite("arrayQualityMetrics") >>>>> >>>>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>>>> Installing Bioconductor version 2.8 packages: >>>>> [1] "arrayQualityMetrics" >>>>> Please wait... >>>>> >>>>> also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' >>>>> ======================================= >>>>> >>>>> it fails, raising the following error: >>>>> >>>>> ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' >>>>> >>>>> >>>>> Best regards, >>>>> -- >>>>> Guillaume Meurice - PhD >>>>> Bioinformaticien >>>>> >>>>> >>>>> >>>>> Le Apr 4, 2011 ? 4:41 PM, Guillaume Meurice a ?crit : >>>>> >>>>>> How nice ! thanks you for the tricks. >>>>>> >>>>>> -- >>>>>> Guillaume Meurice - PhD >>>>>> Bioinformaticien >>>>>> Le Apr 4, 2011 ? 4:09 PM, Steve Lianoglou a ?crit : >>>>>> >>>>>>> Hi Guillaume, >>>>>>> >>>>>>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>>>>>> <guillaume.meurice at="" igr.fr=""> wrote: >>>>>>>> Dear Wolfgang, >>>>>>>> >>>>>>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>>>>>> >>>>>>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>>>>>> >>>>>>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>>>>>> grab it from here: >>>>>>> >>>>>>> http://r.research.att.com/#GUI >>>>>>> >>>>>>> Go to the select the one that's appropriate for your architecture. >>>>>>> >>>>>>> -steve >>>>>>> >>>>>>> -- >>>>>>> Steve Lianoglou >>>>>>> Graduate Student: Computational Systems Biology >>>>>>> | Memorial Sloan-Kettering Cancer Center >>>>>>> | Weill Medical College of Cornell University >>>>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>> >>> >>> [[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 >> >> >> -- >> >> >> 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 > > > [[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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Hi Guillaume, I haven't seen that error before. how did you install Cairo on OSX? Mark On 05/04/2011, at 4:03 PM, Guillaume Meurice wrote: > Hi Mark > > When trying to install separatly Cairo and SVGAnnotation, I got the following error message : > > #################################################################### ############## > source("http://www.bioconductor.org/biocLite.R") > biocLite('Cairo') > Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. > Installing Bioconductor version 2.8 packages: > [1] "Cairo" > Please wait... > > trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz' > Content type 'application/x-gzip' length 78688 bytes (76 Kb) > opened URL > ================================================== > downloaded 76 Kb > > configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. > ERROR: configuration failed for package 'Cairo' > * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/Cairo' > > #################################################################### ############## > > > > and for SVGAnnotation (that seems to need Cairo to be installed) > > #################################################################### ############## > source("http://www.bioconductor.org/biocLite.R") > biocLite("SVGAnnotation") > Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. > Installing Bioconductor version 2.8 packages: > [1] "SVGAnnotation" > Please wait... > > trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/contr ib/SVGAnnotation_0.9-0.tar.gz' > Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb) > opened URL > ================================================== > downloaded 4.5 Mb > > During startup - Warning messages: > 1: Setting LC_CTYPE failed, using "C" > 2: Setting LC_TIME failed, using "C" > 3: Setting LC_MESSAGES failed, using "C" > * installing *source* package 'SVGAnnotation' ... > > q(status = capabilities()["cairo"] == FALSE) > ***** Using the Cairo package. > configure: creating ./config.status > config.status: creating DESCRIPTION > config.status: creating R/config.R > ** R > ** data > ** inst > ** preparing package for lazy loading > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : > there is no package called 'Cairo' > Error : package 'Cairo' could not be loaded > ERROR: lazy loading failed for package 'SVGAnnotation' > * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/SVGAnnotation' > #################################################################### ############## > > > > > Best regards, > -- > Guillaume Meurice - PhD > Bioinformaticien > > Le Apr 5, 2011 à 2:22 AM, Mark Cowley a écrit : > >> Hi Guillame, >> what happens when you do this: >> source("http://www.bioconductor.org/biocLite.R") >> biocLite('Cairo') >> biocLite("SVGAnnotation") >> >> Mark >> >> On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: >> >>> Dear Wolgang, >>> >>> Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: >>> ======================================= >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("arrayQualityMetrics") >>> >>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>> Installing Bioconductor version 2.8 packages: >>> [1] "arrayQualityMetrics" >>> Please wait... >>> >>> also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' >>> ======================================= >>> >>> it fails, raising the following error: >>> >>> ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' >>> >>> >>> Best regards, >>> -- >>> Guillaume Meurice - PhD >>> Bioinformaticien >>> >>> >>> >>> Le Apr 4, 2011 à 4:41 PM, Guillaume Meurice a écrit : >>> >>>> How nice ! thanks you for the tricks. >>>> >>>> -- >>>> Guillaume Meurice - PhD >>>> Bioinformaticien >>>> Le Apr 4, 2011 à 4:09 PM, Steve Lianoglou a écrit : >>>> >>>>> Hi Guillaume, >>>>> >>>>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>>>> <guillaume.meurice@igr.fr> wrote: >>>>>> Dear Wolfgang, >>>>>> >>>>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>>>> >>>>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>>>> >>>>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>>>> grab it from here: >>>>> >>>>> http://r.research.att.com/#GUI >>>>> >>>>> Go to the select the one that's appropriate for your architecture. >>>>> >>>>> -steve >>>>> >>>>> -- >>>>> Steve Lianoglou >>>>> Graduate Student: Computational Systems Biology >>>>> | Memorial Sloan-Kettering Cancer Center >>>>> | Weill Medical College of Cornell University >>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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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Hi Mark, I didn't especially installed cairo, it probably came with developper tools ? -- Guillaume Meurice - PhD Bioinformaticien Le Apr 5, 2011 à 8:33 AM, Mark Cowley a écrit : > Hi Guillaume, > I haven't seen that error before. how did you install Cairo on OSX? > > Mark > > On 05/04/2011, at 4:03 PM, Guillaume Meurice wrote: > >> Hi Mark >> >> When trying to install separatly Cairo and SVGAnnotation, I got the following error message : >> >> ################################################################### ############### >> source("http://www.bioconductor.org/biocLite.R") >> biocLite('Cairo') >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "Cairo" >> Please wait... >> >> trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz' >> Content type 'application/x-gzip' length 78688 bytes (76 Kb) >> opened URL >> ================================================== >> downloaded 76 Kb >> >> configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly. >> ERROR: configuration failed for package 'Cairo' >> * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources /library/Cairo' >> >> ################################################################### ############### >> >> >> >> and for SVGAnnotation (that seems to need Cairo to be installed) >> >> ################################################################### ############### >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("SVGAnnotation") >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "SVGAnnotation" >> Please wait... >> >> trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/cont rib/SVGAnnotation_0.9-0.tar.gz' >> Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb) >> opened URL >> ================================================== >> downloaded 4.5 Mb >> >> During startup - Warning messages: >> 1: Setting LC_CTYPE failed, using "C" >> 2: Setting LC_TIME failed, using "C" >> 3: Setting LC_MESSAGES failed, using "C" >> * installing *source* package 'SVGAnnotation' ... >> > q(status = capabilities()["cairo"] == FALSE) >> ***** Using the Cairo package. >> configure: creating ./config.status >> config.status: creating DESCRIPTION >> config.status: creating R/config.R >> ** R >> ** data >> ** inst >> ** preparing package for lazy loading >> Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : >> there is no package called 'Cairo' >> Error : package 'Cairo' could not be loaded >> ERROR: lazy loading failed for package 'SVGAnnotation' >> * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources /library/SVGAnnotation' >> ################################################################### ############### >> >> >> >> >> Best regards, >> -- >> Guillaume Meurice - PhD >> Bioinformaticien >> >> Le Apr 5, 2011 à 2:22 AM, Mark Cowley a écrit : >> >>> Hi Guillame, >>> what happens when you do this: >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite('Cairo') >>> biocLite("SVGAnnotation") >>> >>> Mark >>> >>> On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote: >>> >>>> Dear Wolgang, >>>> >>>> Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics: >>>> ======================================= >>>> source("http://www.bioconductor.org/biocLite.R") >>>> biocLite("arrayQualityMetrics") >>>> >>>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >>>> Installing Bioconductor version 2.8 packages: >>>> [1] "arrayQualityMetrics" >>>> Please wait... >>>> >>>> also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML' >>>> ======================================= >>>> >>>> it fails, raising the following error: >>>> >>>> ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics' >>>> >>>> >>>> Best regards, >>>> -- >>>> Guillaume Meurice - PhD >>>> Bioinformaticien >>>> >>>> >>>> >>>> Le Apr 4, 2011 à 4:41 PM, Guillaume Meurice a écrit : >>>> >>>>> How nice ! thanks you for the tricks. >>>>> >>>>> -- >>>>> Guillaume Meurice - PhD >>>>> Bioinformaticien >>>>> Le Apr 4, 2011 à 4:09 PM, Steve Lianoglou a écrit : >>>>> >>>>>> Hi Guillaume, >>>>>> >>>>>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice >>>>>> <guillaume.meurice@igr.fr> wrote: >>>>>>> Dear Wolfgang, >>>>>>> >>>>>>> Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(. >>>>>>> >>>>>>> But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode. >>>>>> >>>>>> If you find that you'd rather use the R.app GUI with R-2.13, you can >>>>>> grab it from here: >>>>>> >>>>>> http://r.research.att.com/#GUI >>>>>> >>>>>> Go to the select the one that's appropriate for your architecture. >>>>>> >>>>>> -steve >>>>>> >>>>>> -- >>>>>> Steve Lianoglou >>>>>> Graduate Student: Computational Systems Biology >>>>>> | Memorial Sloan-Kettering Cancer Center >>>>>> | Weill Medical College of Cornell University >>>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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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