ggbio: error when updating to current release version
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@juan-l-mateo-5110
Last seen 10.2 years ago
Dear all, I tried to update the package ggbio from version 1.0.4 to the current release version 1.2.8 but there seems to be an error. I list below the error output and sessionInfo(). I tried also to use the development version (1.3.4) but I get the same problem. Best regards > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.3, ?biocLite for help > biocLite("ggbio") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.3. Installing package(s) 'ggbio' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio_1.2. 8.tar.gz' Content type 'application/x-gzip' length 205262 bytes (200 Kb) opened URL ================================================== downloaded 200 Kb * installing *source* package ?ggbio? ... ** R ** inst ** preparing package for lazy loading Warning: found methods to import for function ?as.list? but not the generic itself Warning: found methods to import for function ?chartr? but not the generic itself Warning: found methods to import for function ?IQR? but not the generic itself Warning: found methods to import for function ?NROW? but not the generic itself Warning: found methods to import for function ?aggregate? but not the generic itself Warning: found methods to import for function ?chartr? but not the generic itself Warning: found methods to import for function ?cor? but not the generic itself Creating a new generic function for ?rescale? in package ?ggbio? Creating a generic function for ?summary? from package ?base? in package ?ggbio? Creating a generic function for ?print? from package ?base? in package ?ggbio? Creating a new generic function for ?xlim? in package ?ggbio? Creating a generic function for ?update? from package ?stats? in package ?ggbio? Creating a new generic function for ?geom_rect? in package ?ggbio? Creating a new generic function for ?geom_segment? in package ?ggbio? Creating a new generic function for ?stat_identity? in package ?ggbio? Error in conformMethod(signature, mnames, fnames, f, fdef, definition) : in method for ?autoplot? with signature ?x="GRanges"?: formal arguments (x = "GRanges", ... = "GRanges") omitted in the method definition cannot be in the signature Error : unable to load R code in package ?ggbio? ERROR: lazy loading failed for package ?ggbio? * removing ?/usr/local/lib/R/site-library/ggbio? * restoring previous ?/usr/local/lib/R/site-library/ggbio? > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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] BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] tools_2.15.0 -- ============================= Juan L. Mateo PhD. Centre for Organismal Studies (COS) - University of Heidelberg Im Neuenheimer Feld 230 69120 Heidelberg, Germany Tel: 0049 (0)6221 54 6493 Fax: 0049 (0)6221 54 5639
BiocInstaller ggbio BiocInstaller ggbio • 2.7k views
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@vincent-j-carey-jr-4
Last seen 9 weeks ago
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Hi, I am unable to confirm a problem; check your additional resources against the session info below > sessionInfo() R version 2.15.0 Patched (2012-03-31 r58891) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 [22] memoise_0.1 munsell_0.3 plyr_1.7.1 [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 [40] zlibbioc_1.2.0 On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo < juan.mateo@cos.uni-heidelberg.de> wrote: > Dear all, > > I tried to update the package ggbio from version 1.0.4 to the current > release version 1.2.8 but there seems to be an error. > I list below the error output and sessionInfo(). > I tried also to use the development version (1.3.4) but I get the same > problem. > > Best regards > > > > source("http://bioconductor.**org/biocLite.R<http: bioconductor.o="" rg="" bioclite.r=""> > ") > BiocInstaller version 1.4.3, ?biocLite for help > > biocLite("ggbio") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.3. > Installing package(s) 'ggbio' > trying URL 'http://www.bioconductor.org/**packages/2.10/bioc/src/** > contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz=""> > ' > Content type 'application/x-gzip' length 205262 bytes (200 Kb) > opened URL > ==============================**==================== > downloaded 200 Kb > > * installing *source* package ‘ggbio’ ... > ** R > ** inst > ** preparing package for lazy loading > Warning: found methods to import for function ‘as.list’ but not the > generic itself > Warning: found methods to import for function ‘chartr’ but not the generic > itself > Warning: found methods to import for function ‘IQR’ but not the generic > itself > Warning: found methods to import for function ‘NROW’ but not the generic > itself > Warning: found methods to import for function ‘aggregate’ but not the > generic itself > Warning: found methods to import for function ‘chartr’ but not the generic > itself > Warning: found methods to import for function ‘cor’ but not the generic > itself > Creating a new generic function for ‘rescale’ in package ‘ggbio’ > Creating a generic function for ‘summary’ from package ‘base’ in package > ‘ggbio’ > Creating a generic function for ‘print’ from package ‘base’ in package > ‘ggbio’ > Creating a new generic function for ‘xlim’ in package ‘ggbio’ > Creating a generic function for ‘update’ from package ‘stats’ in package > ‘ggbio’ > Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ > Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ > Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ > Error in conformMethod(signature, mnames, fnames, f, fdef, definition) : > in method for ‘autoplot’ with signature ‘x="GRanges"’: formal arguments > (x = "GRanges", ... = "GRanges") omitted in the method definition cannot be > in the signature > Error : unable to load R code in package ‘ggbio’ > ERROR: lazy loading failed for package ‘ggbio’ > * removing ‘/usr/local/lib/R/site-**library/ggbio’ > * restoring previous ‘/usr/local/lib/R/site-**library/ggbio’ > > > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > > > -- > ============================= > Juan L. Mateo PhD. > Centre for Organismal Studies (COS) - University of Heidelberg > Im Neuenheimer Feld 230 > 69120 Heidelberg, Germany > Tel: 0049 (0)6221 54 6493 > Fax: 0049 (0)6221 54 5639 > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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Hi Vincent, If I install manually all the packages that are listed in your sessionInfo I can install ggbio but with warnings. These warnings remain when I load the module. Appart from that I have tested several functions of ggbio and they seem to work properly. Thanks for the answer Juan > biocLite("ggbio") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.3. Installing package(s) 'ggbio' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio_1.2. 8.tar.gz' Content type 'application/x-gzip' length 205262 bytes (200 Kb) opened URL ================================================== downloaded 200 Kb * installing *source* package ?ggbio? ... ** R ** inst ** preparing package for lazy loading Warning: found methods to import for function ?as.list? but not the generic itself Warning: found methods to import for function ?chartr? but not the generic itself Warning: found methods to import for function ?IQR? but not the generic itself Warning: found methods to import for function ?NROW? but not the generic itself Warning: found methods to import for function ?aggregate? but not the generic itself Warning: found methods to import for function ?chartr? but not the generic itself Warning: found methods to import for function ?cor? but not the generic itself Creating a new generic function for ?rescale? in package ?ggbio? Creating a generic function for ?summary? from package ?base? in package ?ggbio? Creating a generic function for ?print? from package ?base? in package ?ggbio? Creating a new generic function for ?xlim? in package ?ggbio? Creating a generic function for ?update? from package ?stats? in package ?ggbio? Creating a new generic function for ?geom_rect? in package ?ggbio? Creating a new generic function for ?geom_segment? in package ?ggbio? Creating a new generic function for ?stat_identity? in package ?ggbio? Warning in FUN(X[[1L]], ...) : Created a package name, ?2012-04-18 13:53:39?, when none found ** help *** installing help indices ** building package indices ** installing vignettes ?intro.Rnw? ** testing if installed package can be loaded Warning: found methods to import for function ?as.list? but not the generic itself Warning: found methods to import for function ?chartr? but not the generic itself Warning: found methods to import for function ?IQR? but not the generic itself Warning: found methods to import for function ?NROW? but not the generic itself Warning: found methods to import for function ?aggregate? but not the generic itself Warning: found methods to import for function ?chartr? but not the generic itself Warning: found methods to import for function ?cor? but not the generic itself * DONE (ggbio) The downloaded source packages are in ?/tmp/Rtmp3FIBAU/downloaded_packages? Warning message: installed directory not writable, cannot update packages 'ggbio' > library(ggbio) Loading required package: ggplot2 Attaching package: ?ggbio? The following object(s) are masked from ?package:ggplot2?: geom_rect, geom_segment, stat_identity, xlim Warning messages: 1: found methods to import for function ?as.list? but not the generic itself 2: found methods to import for function ?aggregate? but not the generic itself 3: found methods to import for function ?as.table? but not the generic itself 4: found methods to import for function ?complete.cases? but not the generic itself 5: found methods to import for function ?cor? but not the generic itself 6: found methods to import for function ?diff? but not the generic itself 7: found methods to import for function ?drop? but not the generic itself 8: found methods to import for function ?append? but not the generic itself 9: found methods to import for function ?as.data.frame? but not the generic itself 10: found methods to import for function ?as.list? but not the generic itself > > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 [37] stringr_0.6 survival_2.36-12 tools_2.15.0 [40] VariantAnnotation_1.2.5 XML_3.9-4 On 04/18/2012 12:38 PM, Vincent Carey wrote: > Hi, I am unable to confirm a problem; check your additional resources > against the session info below > > > sessionInfo() > R version 2.15.0 Patched (2012-03-31 r58891) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C > [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 > [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets tools utils methods > [8] base > > other attached packages: > [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 > [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 > [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 > [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 > [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 > [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 > [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 > [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 > [22] memoise_0.1 munsell_0.3 plyr_1.7.1 > [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 > [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 > [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 > [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 > [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 > [40] zlibbioc_1.2.0 > > > On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo > <juan.mateo at="" cos.uni-heidelberg.de=""> <mailto:juan.mateo at="" cos.uni-heidelberg.de="">> wrote: > > Dear all, > > I tried to update the package ggbio from version 1.0.4 to the > current release version 1.2.8 but there seems to be an error. > I list below the error output and sessionInfo(). > I tried also to use the development version (1.3.4) but I get the > same problem. > > Best regards > > > > source("http://bioconductor.__org/biocLite.R > <http: bioconductor.org="" bioclite.r="">") > BiocInstaller version 1.4.3, ?biocLite for help > > biocLite("ggbio") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.3. > Installing package(s) 'ggbio' > trying URL > 'http://www.bioconductor.org/__packages/2.10/bioc/src/__contrib/ ggbio_1.2.8.tar.gz > <http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbi="" o_1.2.8.tar.gz="">' > Content type 'application/x-gzip' length 205262 bytes (200 Kb) > opened URL > ==============================__==================== > downloaded 200 Kb > > * installing *source* package ?ggbio? ... > ** R > ** inst > ** preparing package for lazy loading > Warning: found methods to import for function ?as.list? but not the > generic itself > Warning: found methods to import for function ?chartr? but not the > generic itself > Warning: found methods to import for function ?IQR? but not the > generic itself > Warning: found methods to import for function ?NROW? but not the > generic itself > Warning: found methods to import for function ?aggregate? but not > the generic itself > Warning: found methods to import for function ?chartr? but not the > generic itself > Warning: found methods to import for function ?cor? but not the > generic itself > Creating a new generic function for ?rescale? in package ?ggbio? > Creating a generic function for ?summary? from package ?base? in > package ?ggbio? > Creating a generic function for ?print? from package ?base? in > package ?ggbio? > Creating a new generic function for ?xlim? in package ?ggbio? > Creating a generic function for ?update? from package ?stats? in > package ?ggbio? > Creating a new generic function for ?geom_rect? in package ?ggbio? > Creating a new generic function for ?geom_segment? in package ?ggbio? > Creating a new generic function for ?stat_identity? in package ?ggbio? > Error in conformMethod(signature, mnames, fnames, f, fdef, definition) : > in method for ?autoplot? with signature ?x="GRanges"?: formal > arguments (x = "GRanges", ... = "GRanges") omitted in the method > definition cannot be in the signature > Error : unable to load R code in package ?ggbio? > ERROR: lazy loading failed for package ?ggbio? > * removing ?/usr/local/lib/R/site-__library/ggbio? > * restoring previous ?/usr/local/lib/R/site-__library/ggbio? > > > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > > > -- > ============================= > Juan L. Mateo PhD. > Centre for Organismal Studies (COS) - University of Heidelberg > Im Neuenheimer Feld 230 > 69120 Heidelberg, Germany > Tel: 0049 (0)6221 54 6493 > Fax: 0049 (0)6221 54 5639 > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >
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These warnings are due to a bug in R that is fixed, but we'll have to wait for 2.15.1. Michael On Wed, Apr 18, 2012 at 5:36 AM, Juan L. Mateo < juan.mateo@cos.uni-heidelberg.de> wrote: > Hi Vincent, > > If I install manually all the packages that are listed in your sessionInfo > I can install ggbio but with warnings. These warnings remain when I load > the module. > Appart from that I have tested several functions of ggbio and they seem to > work properly. > > > Thanks for the answer > Juan > > > > biocLite("ggbio") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.3. > Installing package(s) 'ggbio' > trying URL 'http://www.bioconductor.org/**packages/2.10/bioc/src/** > contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz=""> > ' > > Content type 'application/x-gzip' length 205262 bytes (200 Kb) > opened URL > ==============================**==================== > > downloaded 200 Kb > > * installing *source* package ‘ggbio’ ... > ** R > ** inst > ** preparing package for lazy loading > Warning: found methods to import for function ‘as.list’ but not the > generic itself > Warning: found methods to import for function ‘chartr’ but not the generic > itself > Warning: found methods to import for function ‘IQR’ but not the generic > itself > Warning: found methods to import for function ‘NROW’ but not the generic > itself > Warning: found methods to import for function ‘aggregate’ but not the > generic itself > Warning: found methods to import for function ‘chartr’ but not the generic > itself > Warning: found methods to import for function ‘cor’ but not the generic > itself > Creating a new generic function for ‘rescale’ in package ‘ggbio’ > Creating a generic function for ‘summary’ from package ‘base’ in package > ‘ggbio’ > Creating a generic function for ‘print’ from package ‘base’ in package > ‘ggbio’ > Creating a new generic function for ‘xlim’ in package ‘ggbio’ > Creating a generic function for ‘update’ from package ‘stats’ in package > ‘ggbio’ > Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ > Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ > Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ > Warning in FUN(X[[1L]], ...) : > Created a package name, ‘2012-04-18 13:53:39’, when none found > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ‘intro.Rnw’ > ** testing if installed package can be loaded > > Warning: found methods to import for function ‘as.list’ but not the > generic itself > Warning: found methods to import for function ‘chartr’ but not the generic > itself > Warning: found methods to import for function ‘IQR’ but not the generic > itself > Warning: found methods to import for function ‘NROW’ but not the generic > itself > Warning: found methods to import for function ‘aggregate’ but not the > generic itself > Warning: found methods to import for function ‘chartr’ but not the generic > itself > Warning: found methods to import for function ‘cor’ but not the generic > itself > > * DONE (ggbio) > > The downloaded source packages are in > ‘/tmp/Rtmp3FIBAU/downloaded_**packages’ > Warning message: > installed directory not writable, cannot update packages 'ggbio' > > library(ggbio) > Loading required package: ggplot2 > > Attaching package: ‘ggbio’ > > The following object(s) are masked from ‘package:ggplot2’: > > geom_rect, geom_segment, stat_identity, xlim > > Warning messages: > > 1: found methods to import for function ‘as.list’ but not the generic > itself > 2: found methods to import for function ‘aggregate’ but not the generic > itself > 3: found methods to import for function ‘as.table’ but not the generic > itself > 4: found methods to import for function ‘complete.cases’ but not the > generic itself > > 5: found methods to import for function ‘cor’ but not the generic itself > 6: found methods to import for function ‘diff’ but not the generic itself > 7: found methods to import for function ‘drop’ but not the generic itself > 8: found methods to import for function ‘append’ but not the generic itself > 9: found methods to import for function ‘as.data.frame’ but not the > generic itself > 10: found methods to import for function ‘as.list’ but not the generic > itself > > > > > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 > > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 > [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 > [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 > [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 > [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 > [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 > [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 > [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 > [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 > [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 > [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 > [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 > [37] stringr_0.6 survival_2.36-12 tools_2.15.0 > [40] VariantAnnotation_1.2.5 XML_3.9-4 > > > > On 04/18/2012 12:38 PM, Vincent Carey wrote: > >> Hi, I am unable to confirm a problem; check your additional resources >> against the session info below >> >> > sessionInfo() >> R version 2.15.0 Patched (2012-03-31 r58891) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets tools utils methods >> [8] base >> >> other attached packages: >> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >> [40] zlibbioc_1.2.0 >> >> >> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >> <juan.mateo@cos.uni-**heidelberg.de <juan.mateo@cos.uni-="" heidelberg.de=""> >> <mailto:juan.mateo@cos.uni-**heidelberg.de<juan.mateo@cos.uni- heidelberg.de="">>> >> wrote: >> >> Dear all, >> >> I tried to update the package ggbio from version 1.0.4 to the >> current release version 1.2.8 but there seems to be an error. >> I list below the error output and sessionInfo(). >> I tried also to use the development version (1.3.4) but I get the >> same problem. >> >> Best regards >> >> >> > source("http://bioconductor.__**org/biocLite.R >> >> <http: bioconductor.org="" **bioclite.r<http:="" bioconductor.org="" bi="" oclite.r=""> >> >") >> BiocInstaller version 1.4.3, ?biocLite for help >> > biocLite("ggbio") >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.3. >> Installing package(s) 'ggbio' >> trying URL >> 'http://www.bioconductor.org/_**_packages/2.10/bioc/src/__** >> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" __packages="" 2="" .10="" bioc="" src="" __contrib="" ggbio_1.2.8.tar.gz=""> >> >> <http: www.bioconductor.org="" **packages="" 2.10="" bioc="" src="" **="">> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2.1="" 0="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz=""> >> >' >> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >> opened URL >> ==============================**__==================== >> >> downloaded 200 Kb >> >> * installing *source* package ‘ggbio’ ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Warning: found methods to import for function ‘as.list’ but not the >> generic itself >> Warning: found methods to import for function ‘chartr’ but not the >> generic itself >> Warning: found methods to import for function ‘IQR’ but not the >> generic itself >> Warning: found methods to import for function ‘NROW’ but not the >> generic itself >> Warning: found methods to import for function ‘aggregate’ but not >> the generic itself >> Warning: found methods to import for function ‘chartr’ but not the >> generic itself >> Warning: found methods to import for function ‘cor’ but not the >> generic itself >> Creating a new generic function for ‘rescale’ in package ‘ggbio’ >> Creating a generic function for ‘summary’ from package ‘base’ in >> package ‘ggbio’ >> Creating a generic function for ‘print’ from package ‘base’ in >> package ‘ggbio’ >> Creating a new generic function for ‘xlim’ in package ‘ggbio’ >> Creating a generic function for ‘update’ from package ‘stats’ in >> package ‘ggbio’ >> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ >> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ >> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ >> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) >> : >> in method for ‘autoplot’ with signature ‘x="GRanges"’: formal >> arguments (x = "GRanges", ... = "GRanges") omitted in the method >> definition cannot be in the signature >> Error : unable to load R code in package ‘ggbio’ >> ERROR: lazy loading failed for package ‘ggbio’ >> * removing ‘/usr/local/lib/R/site-__**library/ggbio’ >> * restoring previous ‘/usr/local/lib/R/site-__**library/ggbio’ >> >> >> >> >> > sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.0 >> >> >> -- >> ============================= >> Juan L. Mateo PhD. >> Centre for Organismal Studies (COS) - University of Heidelberg >> Im Neuenheimer Feld 230 >> 69120 Heidelberg, Germany >> Tel: 0049 (0)6221 54 6493 >> Fax: 0049 (0)6221 54 5639 >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https: s="" tat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" st="" at.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__** >> conductor<http: news.gmane.org="" gmane.__science.biology.informatics="" .__conductor="">< >> http://news.gmane.org/gmane.**science.biology.informatics.**conduct or<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >> > >> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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On 4/18/2012 5:36 AM, Juan L. Mateo wrote: > Hi Vincent, > > If I install manually all the packages that are listed in your > sessionInfo I can install ggbio but with warnings. These warnings > remain when I load the module. Did your original attempt to install ggbio indicate that some specific packages were out of date and need to be updated? biocLite is supposed to catch these things, so that guessing at which packages are out of date (via Vince's sessionInfo()!) is not necessary. Martin > Appart from that I have tested several functions of ggbio and they > seem to work properly. > > Thanks for the answer > Juan > > > biocLite("ggbio") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.3. > Installing package(s) 'ggbio' > trying URL > 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio_1. 2.8.tar.gz' > Content type 'application/x-gzip' length 205262 bytes (200 Kb) > opened URL > ================================================== > downloaded 200 Kb > > * installing *source* package ?ggbio? ... > ** R > ** inst > ** preparing package for lazy loading > Warning: found methods to import for function ?as.list? but not the > generic itself > Warning: found methods to import for function ?chartr? but not the > generic itself > Warning: found methods to import for function ?IQR? but not the > generic itself > Warning: found methods to import for function ?NROW? but not the > generic itself > Warning: found methods to import for function ?aggregate? but not the > generic itself > Warning: found methods to import for function ?chartr? but not the > generic itself > Warning: found methods to import for function ?cor? but not the > generic itself > Creating a new generic function for ?rescale? in package ?ggbio? > Creating a generic function for ?summary? from package ?base? in > package ?ggbio? > Creating a generic function for ?print? from package ?base? in package > ?ggbio? > Creating a new generic function for ?xlim? in package ?ggbio? > Creating a generic function for ?update? from package ?stats? in > package ?ggbio? > Creating a new generic function for ?geom_rect? in package ?ggbio? > Creating a new generic function for ?geom_segment? in package ?ggbio? > Creating a new generic function for ?stat_identity? in package ?ggbio? > Warning in FUN(X[[1L]], ...) : > Created a package name, ?2012-04-18 13:53:39?, when none found > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ?intro.Rnw? > ** testing if installed package can be loaded > Warning: found methods to import for function ?as.list? but not the > generic itself > Warning: found methods to import for function ?chartr? but not the > generic itself > Warning: found methods to import for function ?IQR? but not the > generic itself > Warning: found methods to import for function ?NROW? but not the > generic itself > Warning: found methods to import for function ?aggregate? but not the > generic itself > Warning: found methods to import for function ?chartr? but not the > generic itself > Warning: found methods to import for function ?cor? but not the > generic itself > > * DONE (ggbio) > > The downloaded source packages are in > ?/tmp/Rtmp3FIBAU/downloaded_packages? > Warning message: > installed directory not writable, cannot update packages 'ggbio' > > library(ggbio) > Loading required package: ggplot2 > > Attaching package: ?ggbio? > > The following object(s) are masked from ?package:ggplot2?: > > geom_rect, geom_segment, stat_identity, xlim > > Warning messages: > 1: found methods to import for function ?as.list? but not the generic > itself > 2: found methods to import for function ?aggregate? but not the > generic itself > 3: found methods to import for function ?as.table? but not the generic > itself > 4: found methods to import for function ?complete.cases? but not the > generic itself > 5: found methods to import for function ?cor? but not the generic itself > 6: found methods to import for function ?diff? but not the generic itself > 7: found methods to import for function ?drop? but not the generic itself > 8: found methods to import for function ?append? but not the generic > itself > 9: found methods to import for function ?as.data.frame? but not the > generic itself > 10: found methods to import for function ?as.list? but not the generic > itself > > > > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 > [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 > [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 > [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 > [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 > [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 > [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 > [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 > [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 > [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 > [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 > [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 > [37] stringr_0.6 survival_2.36-12 tools_2.15.0 > [40] VariantAnnotation_1.2.5 XML_3.9-4 > > > On 04/18/2012 12:38 PM, Vincent Carey wrote: >> Hi, I am unable to confirm a problem; check your additional resources >> against the session info below >> >> > sessionInfo() >> R version 2.15.0 Patched (2012-03-31 r58891) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets tools utils methods >> [8] base >> >> other attached packages: >> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >> [40] zlibbioc_1.2.0 >> >> >> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >> <juan.mateo at="" cos.uni-heidelberg.de="">> <mailto:juan.mateo at="" cos.uni-heidelberg.de="">> wrote: >> >> Dear all, >> >> I tried to update the package ggbio from version 1.0.4 to the >> current release version 1.2.8 but there seems to be an error. >> I list below the error output and sessionInfo(). >> I tried also to use the development version (1.3.4) but I get the >> same problem. >> >> Best regards >> >> >> > source("http://bioconductor.__org/biocLite.R >> <http: bioconductor.org="" bioclite.r="">") >> BiocInstaller version 1.4.3, ?biocLite for help >> > biocLite("ggbio") >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.3. >> Installing package(s) 'ggbio' >> trying URL >> >> 'http://www.bioconductor.org/__packages/2.10/bioc/src/__contrib/ggb io_1.2.8.tar.gz >> <http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_1="" .2.8.tar.gz="">' >> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >> opened URL >> ==============================__==================== >> downloaded 200 Kb >> >> * installing *source* package ?ggbio? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Warning: found methods to import for function ?as.list? but not the >> generic itself >> Warning: found methods to import for function ?chartr? but not the >> generic itself >> Warning: found methods to import for function ?IQR? but not the >> generic itself >> Warning: found methods to import for function ?NROW? but not the >> generic itself >> Warning: found methods to import for function ?aggregate? but not >> the generic itself >> Warning: found methods to import for function ?chartr? but not the >> generic itself >> Warning: found methods to import for function ?cor? but not the >> generic itself >> Creating a new generic function for ?rescale? in package ?ggbio? >> Creating a generic function for ?summary? from package ?base? in >> package ?ggbio? >> Creating a generic function for ?print? from package ?base? in >> package ?ggbio? >> Creating a new generic function for ?xlim? in package ?ggbio? >> Creating a generic function for ?update? from package ?stats? in >> package ?ggbio? >> Creating a new generic function for ?geom_rect? in package ?ggbio? >> Creating a new generic function for ?geom_segment? in package >> ?ggbio? >> Creating a new generic function for ?stat_identity? in package >> ?ggbio? >> Error in conformMethod(signature, mnames, fnames, f, fdef, >> definition) : >> in method for ?autoplot? with signature ?x="GRanges"?: formal >> arguments (x = "GRanges", ... = "GRanges") omitted in the method >> definition cannot be in the signature >> Error : unable to load R code in package ?ggbio? >> ERROR: lazy loading failed for package ?ggbio? >> * removing ?/usr/local/lib/R/site-__library/ggbio? >> * restoring previous ?/usr/local/lib/R/site-__library/ggbio? >> >> >> >> > sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.0 >> >> >> -- >> ============================= >> Juan L. Mateo PhD. >> Centre for Organismal Studies (COS) - University of Heidelberg >> Im Neuenheimer Feld 230 >> 69120 Heidelberg, Germany >> Tel: 0049 (0)6221 54 6493 >> Fax: 0049 (0)6221 54 5639 >> >> _________________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/__listinfo/bioconductor >> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> >> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >> <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 -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
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Hi, I came to this problem when I was updating all my bioconductor packages (biocLite(character(), ask=FALSE)) and I had already the previous version of ggbio installed and working. The update was all right but for ggbio. Best, Juan On 04/18/2012 05:39 PM, Martin Morgan wrote: > On 4/18/2012 5:36 AM, Juan L. Mateo wrote: >> Hi Vincent, >> >> If I install manually all the packages that are listed in your >> sessionInfo I can install ggbio but with warnings. These warnings >> remain when I load the module. > > Did your original attempt to install ggbio indicate that some specific > packages were out of date and need to be updated? biocLite is supposed > to catch these things, so that guessing at which packages are out of > date (via Vince's sessionInfo()!) is not necessary. > > Martin > >> Appart from that I have tested several functions of ggbio and they >> seem to work properly. >> >> Thanks for the answer >> Juan >> >> > biocLite("ggbio") >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.3. >> Installing package(s) 'ggbio' >> trying URL >> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio_1 .2.8.tar.gz' >> >> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >> opened URL >> ================================================== >> downloaded 200 Kb >> >> * installing *source* package ?ggbio? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Warning: found methods to import for function ?as.list? but not the >> generic itself >> Warning: found methods to import for function ?chartr? but not the >> generic itself >> Warning: found methods to import for function ?IQR? but not the >> generic itself >> Warning: found methods to import for function ?NROW? but not the >> generic itself >> Warning: found methods to import for function ?aggregate? but not the >> generic itself >> Warning: found methods to import for function ?chartr? but not the >> generic itself >> Warning: found methods to import for function ?cor? but not the >> generic itself >> Creating a new generic function for ?rescale? in package ?ggbio? >> Creating a generic function for ?summary? from package ?base? in >> package ?ggbio? >> Creating a generic function for ?print? from package ?base? in package >> ?ggbio? >> Creating a new generic function for ?xlim? in package ?ggbio? >> Creating a generic function for ?update? from package ?stats? in >> package ?ggbio? >> Creating a new generic function for ?geom_rect? in package ?ggbio? >> Creating a new generic function for ?geom_segment? in package ?ggbio? >> Creating a new generic function for ?stat_identity? in package ?ggbio? >> Warning in FUN(X[[1L]], ...) : >> Created a package name, ?2012-04-18 13:53:39?, when none found >> ** help >> *** installing help indices >> ** building package indices >> ** installing vignettes >> ?intro.Rnw? >> ** testing if installed package can be loaded >> Warning: found methods to import for function ?as.list? but not the >> generic itself >> Warning: found methods to import for function ?chartr? but not the >> generic itself >> Warning: found methods to import for function ?IQR? but not the >> generic itself >> Warning: found methods to import for function ?NROW? but not the >> generic itself >> Warning: found methods to import for function ?aggregate? but not the >> generic itself >> Warning: found methods to import for function ?chartr? but not the >> generic itself >> Warning: found methods to import for function ?cor? but not the >> generic itself >> >> * DONE (ggbio) >> >> The downloaded source packages are in >> ?/tmp/Rtmp3FIBAU/downloaded_packages? >> Warning message: >> installed directory not writable, cannot update packages 'ggbio' >> > library(ggbio) >> Loading required package: ggplot2 >> >> Attaching package: ?ggbio? >> >> The following object(s) are masked from ?package:ggplot2?: >> >> geom_rect, geom_segment, stat_identity, xlim >> >> Warning messages: >> 1: found methods to import for function ?as.list? but not the generic >> itself >> 2: found methods to import for function ?aggregate? but not the >> generic itself >> 3: found methods to import for function ?as.table? but not the generic >> itself >> 4: found methods to import for function ?complete.cases? but not the >> generic itself >> 5: found methods to import for function ?cor? but not the generic itself >> 6: found methods to import for function ?diff? but not the generic itself >> 7: found methods to import for function ?drop? but not the generic itself >> 8: found methods to import for function ?append? but not the generic >> itself >> 9: found methods to import for function ?as.data.frame? but not the >> generic itself >> 10: found methods to import for function ?as.list? but not the generic >> itself >> > >> >> >> > sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >> [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 >> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >> [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 >> [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 >> [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 >> [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 >> [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >> [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 >> [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 >> [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 >> [37] stringr_0.6 survival_2.36-12 tools_2.15.0 >> [40] VariantAnnotation_1.2.5 XML_3.9-4 >> >> >> On 04/18/2012 12:38 PM, Vincent Carey wrote: >>> Hi, I am unable to confirm a problem; check your additional resources >>> against the session info below >>> >>> > sessionInfo() >>> R version 2.15.0 Patched (2012-03-31 r58891) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >>> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >>> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets tools utils methods >>> [8] base >>> >>> other attached packages: >>> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >>> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >>> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >>> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >>> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >>> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >>> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >>> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >>> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >>> [40] zlibbioc_1.2.0 >>> >>> >>> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >>> <juan.mateo at="" cos.uni-heidelberg.de="">>> <mailto:juan.mateo at="" cos.uni-heidelberg.de="">> wrote: >>> >>> Dear all, >>> >>> I tried to update the package ggbio from version 1.0.4 to the >>> current release version 1.2.8 but there seems to be an error. >>> I list below the error output and sessionInfo(). >>> I tried also to use the development version (1.3.4) but I get the >>> same problem. >>> >>> Best regards >>> >>> >>> > source("http://bioconductor.__org/biocLite.R >>> <http: bioconductor.org="" bioclite.r="">") >>> BiocInstaller version 1.4.3, ?biocLite for help >>> > biocLite("ggbio") >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.4.3. >>> Installing package(s) 'ggbio' >>> trying URL >>> 'http://www.bioconductor.org/__packages/2.10/bioc/src/__contrib/gg bio_1.2.8.tar.gz >>> >>> <http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_="" 1.2.8.tar.gz="">' >>> >>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>> opened URL >>> ==============================__==================== >>> downloaded 200 Kb >>> >>> * installing *source* package ?ggbio? ... >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> Warning: found methods to import for function ?as.list? but not the >>> generic itself >>> Warning: found methods to import for function ?chartr? but not the >>> generic itself >>> Warning: found methods to import for function ?IQR? but not the >>> generic itself >>> Warning: found methods to import for function ?NROW? but not the >>> generic itself >>> Warning: found methods to import for function ?aggregate? but not >>> the generic itself >>> Warning: found methods to import for function ?chartr? but not the >>> generic itself >>> Warning: found methods to import for function ?cor? but not the >>> generic itself >>> Creating a new generic function for ?rescale? in package ?ggbio? >>> Creating a generic function for ?summary? from package ?base? in >>> package ?ggbio? >>> Creating a generic function for ?print? from package ?base? in >>> package ?ggbio? >>> Creating a new generic function for ?xlim? in package ?ggbio? >>> Creating a generic function for ?update? from package ?stats? in >>> package ?ggbio? >>> Creating a new generic function for ?geom_rect? in package ?ggbio? >>> Creating a new generic function for ?geom_segment? in package ?ggbio? >>> Creating a new generic function for ?stat_identity? in package ?ggbio? >>> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) : >>> in method for ?autoplot? with signature ?x="GRanges"?: formal >>> arguments (x = "GRanges", ... = "GRanges") omitted in the method >>> definition cannot be in the signature >>> Error : unable to load R code in package ?ggbio? >>> ERROR: lazy loading failed for package ?ggbio? >>> * removing ?/usr/local/lib/R/site-__library/ggbio? >>> * restoring previous ?/usr/local/lib/R/site-__library/ggbio? >>> >>> >>> >>> > sessionInfo() >>> R version 2.15.0 (2012-03-30) >>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.15.0 >>> >>> >>> -- >>> ============================= >>> Juan L. Mateo PhD. >>> Centre for Organismal Studies (COS) - University of Heidelberg >>> Im Neuenheimer Feld 230 >>> 69120 Heidelberg, Germany >>> Tel: 0049 (0)6221 54 6493 >>> Fax: 0049 (0)6221 54 5639 >>> >>> _________________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>> <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 > >
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On 4/18/2012 8:44 AM, Juan L. Mateo wrote: > Hi, > I came to this problem when I was updating all my bioconductor > packages (biocLite(character(), ask=FALSE)) and I had already the > previous version of ggbio installed and working. The update was all > right but for ggbio. I guess I'm trying to understand why biocLite didn't update the packages that ggbio depends on, and why you had to do that manually? Which package was out-of-date after biocLite(character(), ask=FALSE) that needed to be updated manually? Martin > > Best, > Juan > > On 04/18/2012 05:39 PM, Martin Morgan wrote: >> On 4/18/2012 5:36 AM, Juan L. Mateo wrote: >>> Hi Vincent, >>> >>> If I install manually all the packages that are listed in your >>> sessionInfo I can install ggbio but with warnings. These warnings >>> remain when I load the module. >> >> Did your original attempt to install ggbio indicate that some specific >> packages were out of date and need to be updated? biocLite is supposed >> to catch these things, so that guessing at which packages are out of >> date (via Vince's sessionInfo()!) is not necessary. >> >> Martin >> >>> Appart from that I have tested several functions of ggbio and they >>> seem to work properly. >>> >>> Thanks for the answer >>> Juan >>> >>> > biocLite("ggbio") >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.4.3. >>> Installing package(s) 'ggbio' >>> trying URL >>> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio_ 1.2.8.tar.gz' >>> >>> >>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>> opened URL >>> ================================================== >>> downloaded 200 Kb >>> >>> * installing *source* package ?ggbio? ... >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> Warning: found methods to import for function ?as.list? but not the >>> generic itself >>> Warning: found methods to import for function ?chartr? but not the >>> generic itself >>> Warning: found methods to import for function ?IQR? but not the >>> generic itself >>> Warning: found methods to import for function ?NROW? but not the >>> generic itself >>> Warning: found methods to import for function ?aggregate? but not the >>> generic itself >>> Warning: found methods to import for function ?chartr? but not the >>> generic itself >>> Warning: found methods to import for function ?cor? but not the >>> generic itself >>> Creating a new generic function for ?rescale? in package ?ggbio? >>> Creating a generic function for ?summary? from package ?base? in >>> package ?ggbio? >>> Creating a generic function for ?print? from package ?base? in package >>> ?ggbio? >>> Creating a new generic function for ?xlim? in package ?ggbio? >>> Creating a generic function for ?update? from package ?stats? in >>> package ?ggbio? >>> Creating a new generic function for ?geom_rect? in package ?ggbio? >>> Creating a new generic function for ?geom_segment? in package ?ggbio? >>> Creating a new generic function for ?stat_identity? in package ?ggbio? >>> Warning in FUN(X[[1L]], ...) : >>> Created a package name, ?2012-04-18 13:53:39?, when none found >>> ** help >>> *** installing help indices >>> ** building package indices >>> ** installing vignettes >>> ?intro.Rnw? >>> ** testing if installed package can be loaded >>> Warning: found methods to import for function ?as.list? but not the >>> generic itself >>> Warning: found methods to import for function ?chartr? but not the >>> generic itself >>> Warning: found methods to import for function ?IQR? but not the >>> generic itself >>> Warning: found methods to import for function ?NROW? but not the >>> generic itself >>> Warning: found methods to import for function ?aggregate? but not the >>> generic itself >>> Warning: found methods to import for function ?chartr? but not the >>> generic itself >>> Warning: found methods to import for function ?cor? but not the >>> generic itself >>> >>> * DONE (ggbio) >>> >>> The downloaded source packages are in >>> ?/tmp/Rtmp3FIBAU/downloaded_packages? >>> Warning message: >>> installed directory not writable, cannot update packages 'ggbio' >>> > library(ggbio) >>> Loading required package: ggplot2 >>> >>> Attaching package: ?ggbio? >>> >>> The following object(s) are masked from ?package:ggplot2?: >>> >>> geom_rect, geom_segment, stat_identity, xlim >>> >>> Warning messages: >>> 1: found methods to import for function ?as.list? but not the generic >>> itself >>> 2: found methods to import for function ?aggregate? but not the >>> generic itself >>> 3: found methods to import for function ?as.table? but not the generic >>> itself >>> 4: found methods to import for function ?complete.cases? but not the >>> generic itself >>> 5: found methods to import for function ?cor? but not the generic >>> itself >>> 6: found methods to import for function ?diff? but not the generic >>> itself >>> 7: found methods to import for function ?drop? but not the generic >>> itself >>> 8: found methods to import for function ?append? but not the generic >>> itself >>> 9: found methods to import for function ?as.data.frame? but not the >>> generic itself >>> 10: found methods to import for function ?as.list? but not the generic >>> itself >>> > >>> >>> >>> > sessionInfo() >>> R version 2.15.0 (2012-03-30) >>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>> [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 >>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>> [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 >>> [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 >>> [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 >>> [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 >>> [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >>> [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 >>> [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 >>> [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 >>> [37] stringr_0.6 survival_2.36-12 tools_2.15.0 >>> [40] VariantAnnotation_1.2.5 XML_3.9-4 >>> >>> >>> On 04/18/2012 12:38 PM, Vincent Carey wrote: >>>> Hi, I am unable to confirm a problem; check your additional resources >>>> against the session info below >>>> >>>> > sessionInfo() >>>> R version 2.15.0 Patched (2012-03-31 r58891) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >>>> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >>>> [7] LC_PAPER=C LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices datasets tools utils methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >>>> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >>>> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >>>> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >>>> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >>>> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >>>> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >>>> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >>>> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >>>> [40] zlibbioc_1.2.0 >>>> >>>> >>>> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >>>> <juan.mateo at="" cos.uni-heidelberg.de="">>>> <mailto:juan.mateo at="" cos.uni-heidelberg.de="">> wrote: >>>> >>>> Dear all, >>>> >>>> I tried to update the package ggbio from version 1.0.4 to the >>>> current release version 1.2.8 but there seems to be an error. >>>> I list below the error output and sessionInfo(). >>>> I tried also to use the development version (1.3.4) but I get the >>>> same problem. >>>> >>>> Best regards >>>> >>>> >>>> > source("http://bioconductor.__org/biocLite.R >>>> <http: bioconductor.org="" bioclite.r="">") >>>> BiocInstaller version 1.4.3, ?biocLite for help >>>> > biocLite("ggbio") >>>> BioC_mirror: http://bioconductor.org >>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>> Installing package(s) 'ggbio' >>>> trying URL >>>> 'http://www.bioconductor.org/__packages/2.10/bioc/src/__contrib/g gbio_1.2.8.tar.gz >>>> >>>> >>>> <http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio="" _1.2.8.tar.gz="">' >>>> >>>> >>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>> opened URL >>>> ==============================__==================== >>>> downloaded 200 Kb >>>> >>>> * installing *source* package ?ggbio? ... >>>> ** R >>>> ** inst >>>> ** preparing package for lazy loading >>>> Warning: found methods to import for function ?as.list? but not the >>>> generic itself >>>> Warning: found methods to import for function ?chartr? but not the >>>> generic itself >>>> Warning: found methods to import for function ?IQR? but not the >>>> generic itself >>>> Warning: found methods to import for function ?NROW? but not the >>>> generic itself >>>> Warning: found methods to import for function ?aggregate? but not >>>> the generic itself >>>> Warning: found methods to import for function ?chartr? but not the >>>> generic itself >>>> Warning: found methods to import for function ?cor? but not the >>>> generic itself >>>> Creating a new generic function for ?rescale? in package ?ggbio? >>>> Creating a generic function for ?summary? from package ?base? in >>>> package ?ggbio? >>>> Creating a generic function for ?print? from package ?base? in >>>> package ?ggbio? >>>> Creating a new generic function for ?xlim? in package ?ggbio? >>>> Creating a generic function for ?update? from package ?stats? in >>>> package ?ggbio? >>>> Creating a new generic function for ?geom_rect? in package ?ggbio? >>>> Creating a new generic function for ?geom_segment? in package ?ggbio? >>>> Creating a new generic function for ?stat_identity? in package ?ggbio? >>>> Error in conformMethod(signature, mnames, fnames, f, fdef, >>>> definition) : >>>> in method for ?autoplot? with signature ?x="GRanges"?: formal >>>> arguments (x = "GRanges", ... = "GRanges") omitted in the method >>>> definition cannot be in the signature >>>> Error : unable to load R code in package ?ggbio? >>>> ERROR: lazy loading failed for package ?ggbio? >>>> * removing ?/usr/local/lib/R/site-__library/ggbio? >>>> * restoring previous ?/usr/local/lib/R/site-__library/ggbio? >>>> >>>> >>>> >>>> > sessionInfo() >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tools_2.15.0 >>>> >>>> >>>> -- >>>> ============================= >>>> Juan L. Mateo PhD. >>>> Centre for Organismal Studies (COS) - University of Heidelberg >>>> Im Neuenheimer Feld 230 >>>> 69120 Heidelberg, Germany >>>> Tel: 0049 (0)6221 54 6493 >>>> Fax: 0049 (0)6221 54 5639 >>>> >>>> _________________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>> <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 >> >> -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
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Entering edit mode
On Wed, Apr 18, 2012 at 10:46 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 4/18/2012 8:44 AM, Juan L. Mateo wrote: > >> Hi, >> I came to this problem when I was updating all my bioconductor packages >> (biocLite(character(), ask=FALSE)) and I had already the previous version >> of ggbio installed and working. The update was all right but for ggbio. >> > > I guess I'm trying to understand why biocLite didn't update the packages > that ggbio depends on, and why you had to do that manually? Which package > was out-of-date after biocLite(character(), ask=FALSE) that needed to be > updated manually? > > I can not produce the error on my laptop, so I am not sure what happens here, I may need to add some proper (>=..) to my DESCRIPTION hopefully this could fix the problem. Usually with a update on ggbio, there will be a update in biovizBase too, at least biovizBase should be updated at the same time with ggbio (automatically). Martin > > >> Best, >> Juan >> >> On 04/18/2012 05:39 PM, Martin Morgan wrote: >> >>> On 4/18/2012 5:36 AM, Juan L. Mateo wrote: >>> >>>> Hi Vincent, >>>> >>>> If I install manually all the packages that are listed in your >>>> sessionInfo I can install ggbio but with warnings. These warnings >>>> remain when I load the module. >>>> >>> >>> Did your original attempt to install ggbio indicate that some specific >>> packages were out of date and need to be updated? biocLite is supposed >>> to catch these things, so that guessing at which packages are out of >>> date (via Vince's sessionInfo()!) is not necessary. >>> >>> Martin >>> >>> Appart from that I have tested several functions of ggbio and they >>>> seem to work properly. >>>> >>>> Thanks for the answer >>>> Juan >>>> >>>> > biocLite("ggbio") >>>> BioC_mirror: http://bioconductor.org >>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>> Installing package(s) 'ggbio' >>>> trying URL >>>> 'http://www.bioconductor.org/**packages/2.10/bioc/src/** >>>> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2="" .10="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz="">' >>>> >>>> >>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>> opened URL >>>> ==============================**==================== >>>> downloaded 200 Kb >>>> >>>> * installing *source* package ‘ggbio’ ... >>>> ** R >>>> ** inst >>>> ** preparing package for lazy loading >>>> Warning: found methods to import for function ‘as.list’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘chartr’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘IQR’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘NROW’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘aggregate’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘chartr’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘cor’ but not the >>>> generic itself >>>> Creating a new generic function for ‘rescale’ in package ‘ggbio’ >>>> Creating a generic function for ‘summary’ from package ‘base’ in >>>> package ‘ggbio’ >>>> Creating a generic function for ‘print’ from package ‘base’ in package >>>> ‘ggbio’ >>>> Creating a new generic function for ‘xlim’ in package ‘ggbio’ >>>> Creating a generic function for ‘update’ from package ‘stats’ in >>>> package ‘ggbio’ >>>> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ >>>> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ >>>> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ >>>> Warning in FUN(X[[1L]], ...) : >>>> Created a package name, ‘2012-04-18 13:53:39’, when none found >>>> ** help >>>> *** installing help indices >>>> ** building package indices >>>> ** installing vignettes >>>> ‘intro.Rnw’ >>>> ** testing if installed package can be loaded >>>> Warning: found methods to import for function ‘as.list’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘chartr’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘IQR’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘NROW’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘aggregate’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘chartr’ but not the >>>> generic itself >>>> Warning: found methods to import for function ‘cor’ but not the >>>> generic itself >>>> >>>> * DONE (ggbio) >>>> >>>> The downloaded source packages are in >>>> ‘/tmp/Rtmp3FIBAU/downloaded_**packages’ >>>> Warning message: >>>> installed directory not writable, cannot update packages 'ggbio' >>>> > library(ggbio) >>>> Loading required package: ggplot2 >>>> >>>> Attaching package: ‘ggbio’ >>>> >>>> The following object(s) are masked from ‘package:ggplot2’: >>>> >>>> geom_rect, geom_segment, stat_identity, xlim >>>> >>>> Warning messages: >>>> 1: found methods to import for function ‘as.list’ but not the generic >>>> itself >>>> 2: found methods to import for function ‘aggregate’ but not the >>>> generic itself >>>> 3: found methods to import for function ‘as.table’ but not the generic >>>> itself >>>> 4: found methods to import for function ‘complete.cases’ but not the >>>> generic itself >>>> 5: found methods to import for function ‘cor’ but not the generic itself >>>> 6: found methods to import for function ‘diff’ but not the generic >>>> itself >>>> 7: found methods to import for function ‘drop’ but not the generic >>>> itself >>>> 8: found methods to import for function ‘append’ but not the generic >>>> itself >>>> 9: found methods to import for function ‘as.data.frame’ but not the >>>> generic itself >>>> 10: found methods to import for function ‘as.list’ but not the generic >>>> itself >>>> > >>>> >>>> >>>> > sessionInfo() >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>> [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 >>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>> [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 >>>> [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 >>>> [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 >>>> [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 >>>> [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >>>> [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 >>>> [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 >>>> [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 >>>> [37] stringr_0.6 survival_2.36-12 tools_2.15.0 >>>> [40] VariantAnnotation_1.2.5 XML_3.9-4 >>>> >>>> >>>> On 04/18/2012 12:38 PM, Vincent Carey wrote: >>>> >>>>> Hi, I am unable to confirm a problem; check your additional resources >>>>> against the session info below >>>>> >>>>> > sessionInfo() >>>>> R version 2.15.0 Patched (2012-03-31 r58891) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >>>>> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >>>>> [7] LC_PAPER=C LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices datasets tools utils methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>>> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>>> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >>>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>>> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >>>>> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >>>>> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >>>>> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >>>>> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >>>>> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >>>>> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >>>>> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >>>>> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >>>>> [40] zlibbioc_1.2.0 >>>>> >>>>> >>>>> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >>>>> <juan.mateo@cos.uni-**heidelberg.de <juan.mateo@cos.uni-="" heidelberg.de=""> >>>>> <mailto:juan.mateo@cos.uni-**heidelberg.de<juan.mateo@cos.uni- heidelberg.de="">>> >>>>> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I tried to update the package ggbio from version 1.0.4 to the >>>>> current release version 1.2.8 but there seems to be an error. >>>>> I list below the error output and sessionInfo(). >>>>> I tried also to use the development version (1.3.4) but I get the >>>>> same problem. >>>>> >>>>> Best regards >>>>> >>>>> >>>>> > source("http://bioconductor.__**org/biocLite.R >>>>> <http: bioconductor.org="" **bioclite.r<http:="" bioconductor.org="" bi="" oclite.r=""> >>>>> >") >>>>> BiocInstaller version 1.4.3, ?biocLite for help >>>>> > biocLite("ggbio") >>>>> BioC_mirror: http://bioconductor.org >>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>> Installing package(s) 'ggbio' >>>>> trying URL >>>>> 'http://www.bioconductor.org/_**_packages/2.10/bioc/src/__** >>>>> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" __package="" s="" 2.10="" bioc="" src="" __contrib="" ggbio_1.2.8.tar.gz=""> >>>>> >>>>> <http: www.bioconductor.org="" **packages="" 2.10="" bioc="" src="" **="">>>>> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz="">>' >>>>> >>>>> >>>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>>> opened URL >>>>> ==============================**__==================== >>>>> downloaded 200 Kb >>>>> >>>>> * installing *source* package ‘ggbio’ ... >>>>> ** R >>>>> ** inst >>>>> ** preparing package for lazy loading >>>>> Warning: found methods to import for function ‘as.list’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘IQR’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘NROW’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘aggregate’ but not >>>>> the generic itself >>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘cor’ but not the >>>>> generic itself >>>>> Creating a new generic function for ‘rescale’ in package ‘ggbio’ >>>>> Creating a generic function for ‘summary’ from package ‘base’ in >>>>> package ‘ggbio’ >>>>> Creating a generic function for ‘print’ from package ‘base’ in >>>>> package ‘ggbio’ >>>>> Creating a new generic function for ‘xlim’ in package ‘ggbio’ >>>>> Creating a generic function for ‘update’ from package ‘stats’ in >>>>> package ‘ggbio’ >>>>> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ >>>>> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ >>>>> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ >>>>> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) >>>>> : >>>>> in method for ‘autoplot’ with signature ‘x="GRanges"’: formal >>>>> arguments (x = "GRanges", ... = "GRanges") omitted in the method >>>>> definition cannot be in the signature >>>>> Error : unable to load R code in package ‘ggbio’ >>>>> ERROR: lazy loading failed for package ‘ggbio’ >>>>> * removing ‘/usr/local/lib/R/site-__**library/ggbio’ >>>>> * restoring previous ‘/usr/local/lib/R/site-__**library/ggbio’ >>>>> >>>>> >>>>> >>>>> > sessionInfo() >>>>> R version 2.15.0 (2012-03-30) >>>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.15.0 >>>>> >>>>> >>>>> -- >>>>> ============================= >>>>> Juan L. Mateo PhD. >>>>> Centre for Organismal Studies (COS) - University of Heidelberg >>>>> Im Neuenheimer Feld 230 >>>>> 69120 Heidelberg, Germany >>>>> Tel: 0049 (0)6221 54 6493 >>>>> Fax: 0049 (0)6221 54 5639 >>>>> >>>>> ______________________________**___________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >>>>> > >>>>> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https: s="" tat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >>>>> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" st="" at.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>> > >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.__**science.biology.informatics.__** >>>>> conductor<http: news.gmane.org="" gmane.__science.biology.informat="" ics.__conductor=""> >>>>> <http: news.gmane.org="" gmane.**science.biology.informatics.**con="" ductor<http:="" news.gmane.org="" gmane.science.biology.informatics.conduct="" or=""> >>>>> > >>>>> >>>>> >>>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.**science.biology.informatics.**condu ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>> >>> >>> > > -- > Dr. Martin Morgan, PhD > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]
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Hi, I don't know which one (or ones) of the new packages is essential because I installed all of them at once and not one by one to check the result of trying to update ggbio. Since this problem could not be reproduced, I guess that it is a specific misconfiguration of my system but I can't tell which. After I run the update command non of my packages were outdated, apart from ggbio, so everything went fine even for the packages that ggbio 1.0.4 depends on. Best, Juan On 04/18/2012 05:46 PM, Martin Morgan wrote: > On 4/18/2012 8:44 AM, Juan L. Mateo wrote: >> Hi, >> I came to this problem when I was updating all my bioconductor >> packages (biocLite(character(), ask=FALSE)) and I had already the >> previous version of ggbio installed and working. The update was all >> right but for ggbio. > > I guess I'm trying to understand why biocLite didn't update the packages > that ggbio depends on, and why you had to do that manually? Which > package was out-of-date after biocLite(character(), ask=FALSE) that > needed to be updated manually? > > Martin >> >> Best, >> Juan >> >> On 04/18/2012 05:39 PM, Martin Morgan wrote: >>> On 4/18/2012 5:36 AM, Juan L. Mateo wrote: >>>> Hi Vincent, >>>> >>>> If I install manually all the packages that are listed in your >>>> sessionInfo I can install ggbio but with warnings. These warnings >>>> remain when I load the module. >>> >>> Did your original attempt to install ggbio indicate that some specific >>> packages were out of date and need to be updated? biocLite is supposed >>> to catch these things, so that guessing at which packages are out of >>> date (via Vince's sessionInfo()!) is not necessary. >>> >>> Martin >>> >>>> Appart from that I have tested several functions of ggbio and they >>>> seem to work properly. >>>> >>>> Thanks for the answer >>>> Juan >>>> >>>> > biocLite("ggbio") >>>> BioC_mirror: http://bioconductor.org >>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>> Installing package(s) 'ggbio' >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio _1.2.8.tar.gz' >>>> >>>> >>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>> opened URL >>>> ================================================== >>>> downloaded 200 Kb >>>> >>>> * installing *source* package ?ggbio? ... >>>> ** R >>>> ** inst >>>> ** preparing package for lazy loading >>>> Warning: found methods to import for function ?as.list? but not the >>>> generic itself >>>> Warning: found methods to import for function ?chartr? but not the >>>> generic itself >>>> Warning: found methods to import for function ?IQR? but not the >>>> generic itself >>>> Warning: found methods to import for function ?NROW? but not the >>>> generic itself >>>> Warning: found methods to import for function ?aggregate? but not the >>>> generic itself >>>> Warning: found methods to import for function ?chartr? but not the >>>> generic itself >>>> Warning: found methods to import for function ?cor? but not the >>>> generic itself >>>> Creating a new generic function for ?rescale? in package ?ggbio? >>>> Creating a generic function for ?summary? from package ?base? in >>>> package ?ggbio? >>>> Creating a generic function for ?print? from package ?base? in package >>>> ?ggbio? >>>> Creating a new generic function for ?xlim? in package ?ggbio? >>>> Creating a generic function for ?update? from package ?stats? in >>>> package ?ggbio? >>>> Creating a new generic function for ?geom_rect? in package ?ggbio? >>>> Creating a new generic function for ?geom_segment? in package ?ggbio? >>>> Creating a new generic function for ?stat_identity? in package ?ggbio? >>>> Warning in FUN(X[[1L]], ...) : >>>> Created a package name, ?2012-04-18 13:53:39?, when none found >>>> ** help >>>> *** installing help indices >>>> ** building package indices >>>> ** installing vignettes >>>> ?intro.Rnw? >>>> ** testing if installed package can be loaded >>>> Warning: found methods to import for function ?as.list? but not the >>>> generic itself >>>> Warning: found methods to import for function ?chartr? but not the >>>> generic itself >>>> Warning: found methods to import for function ?IQR? but not the >>>> generic itself >>>> Warning: found methods to import for function ?NROW? but not the >>>> generic itself >>>> Warning: found methods to import for function ?aggregate? but not the >>>> generic itself >>>> Warning: found methods to import for function ?chartr? but not the >>>> generic itself >>>> Warning: found methods to import for function ?cor? but not the >>>> generic itself >>>> >>>> * DONE (ggbio) >>>> >>>> The downloaded source packages are in >>>> ?/tmp/Rtmp3FIBAU/downloaded_packages? >>>> Warning message: >>>> installed directory not writable, cannot update packages 'ggbio' >>>> > library(ggbio) >>>> Loading required package: ggplot2 >>>> >>>> Attaching package: ?ggbio? >>>> >>>> The following object(s) are masked from ?package:ggplot2?: >>>> >>>> geom_rect, geom_segment, stat_identity, xlim >>>> >>>> Warning messages: >>>> 1: found methods to import for function ?as.list? but not the generic >>>> itself >>>> 2: found methods to import for function ?aggregate? but not the >>>> generic itself >>>> 3: found methods to import for function ?as.table? but not the generic >>>> itself >>>> 4: found methods to import for function ?complete.cases? but not the >>>> generic itself >>>> 5: found methods to import for function ?cor? but not the generic >>>> itself >>>> 6: found methods to import for function ?diff? but not the generic >>>> itself >>>> 7: found methods to import for function ?drop? but not the generic >>>> itself >>>> 8: found methods to import for function ?append? but not the generic >>>> itself >>>> 9: found methods to import for function ?as.data.frame? but not the >>>> generic itself >>>> 10: found methods to import for function ?as.list? but not the generic >>>> itself >>>> > >>>> >>>> >>>> > sessionInfo() >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>> [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 >>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>> [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 >>>> [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 >>>> [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 >>>> [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 >>>> [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >>>> [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 >>>> [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 >>>> [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 >>>> [37] stringr_0.6 survival_2.36-12 tools_2.15.0 >>>> [40] VariantAnnotation_1.2.5 XML_3.9-4 >>>> >>>> >>>> On 04/18/2012 12:38 PM, Vincent Carey wrote: >>>>> Hi, I am unable to confirm a problem; check your additional resources >>>>> against the session info below >>>>> >>>>> > sessionInfo() >>>>> R version 2.15.0 Patched (2012-03-31 r58891) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >>>>> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >>>>> [7] LC_PAPER=C LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices datasets tools utils methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>>> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>>> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >>>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>>> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >>>>> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >>>>> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >>>>> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >>>>> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >>>>> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >>>>> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >>>>> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >>>>> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >>>>> [40] zlibbioc_1.2.0 >>>>> >>>>> >>>>> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >>>>> <juan.mateo at="" cos.uni-heidelberg.de="">>>>> <mailto:juan.mateo at="" cos.uni-heidelberg.de="">> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I tried to update the package ggbio from version 1.0.4 to the >>>>> current release version 1.2.8 but there seems to be an error. >>>>> I list below the error output and sessionInfo(). >>>>> I tried also to use the development version (1.3.4) but I get the >>>>> same problem. >>>>> >>>>> Best regards >>>>> >>>>> >>>>> > source("http://bioconductor.__org/biocLite.R >>>>> <http: bioconductor.org="" bioclite.r="">") >>>>> BiocInstaller version 1.4.3, ?biocLite for help >>>>> > biocLite("ggbio") >>>>> BioC_mirror: http://bioconductor.org >>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>> Installing package(s) 'ggbio' >>>>> trying URL >>>>> 'http://www.bioconductor.org/__packages/2.10/bioc/src/__contrib/ ggbio_1.2.8.tar.gz >>>>> >>>>> >>>>> <http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbi="" o_1.2.8.tar.gz="">' >>>>> >>>>> >>>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>>> opened URL >>>>> ==============================__==================== >>>>> downloaded 200 Kb >>>>> >>>>> * installing *source* package ?ggbio? ... >>>>> ** R >>>>> ** inst >>>>> ** preparing package for lazy loading >>>>> Warning: found methods to import for function ?as.list? but not the >>>>> generic itself >>>>> Warning: found methods to import for function ?chartr? but not the >>>>> generic itself >>>>> Warning: found methods to import for function ?IQR? but not the >>>>> generic itself >>>>> Warning: found methods to import for function ?NROW? but not the >>>>> generic itself >>>>> Warning: found methods to import for function ?aggregate? but not >>>>> the generic itself >>>>> Warning: found methods to import for function ?chartr? but not the >>>>> generic itself >>>>> Warning: found methods to import for function ?cor? but not the >>>>> generic itself >>>>> Creating a new generic function for ?rescale? in package ?ggbio? >>>>> Creating a generic function for ?summary? from package ?base? in >>>>> package ?ggbio? >>>>> Creating a generic function for ?print? from package ?base? in >>>>> package ?ggbio? >>>>> Creating a new generic function for ?xlim? in package ?ggbio? >>>>> Creating a generic function for ?update? from package ?stats? in >>>>> package ?ggbio? >>>>> Creating a new generic function for ?geom_rect? in package ?ggbio? >>>>> Creating a new generic function for ?geom_segment? in package ?ggbio? >>>>> Creating a new generic function for ?stat_identity? in package ?ggbio? >>>>> Error in conformMethod(signature, mnames, fnames, f, fdef, >>>>> definition) : >>>>> in method for ?autoplot? with signature ?x="GRanges"?: formal >>>>> arguments (x = "GRanges", ... = "GRanges") omitted in the method >>>>> definition cannot be in the signature >>>>> Error : unable to load R code in package ?ggbio? >>>>> ERROR: lazy loading failed for package ?ggbio? >>>>> * removing ?/usr/local/lib/R/site-__library/ggbio? >>>>> * restoring previous ?/usr/local/lib/R/site-__library/ggbio? >>>>> >>>>> >>>>> >>>>> > sessionInfo() >>>>> R version 2.15.0 (2012-03-30) >>>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.15.0 >>>>> >>>>> >>>>> -- >>>>> ============================= >>>>> Juan L. Mateo PhD. >>>>> Centre for Organismal Studies (COS) - University of Heidelberg >>>>> Im Neuenheimer Feld 230 >>>>> 69120 Heidelberg, Germany >>>>> Tel: 0049 (0)6221 54 6493 >>>>> Fax: 0049 (0)6221 54 5639 >>>>> >>>>> _________________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>>> <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 >>> >>> > >
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I typically have the same problem with ggbio. Never works as an update for me. On Wed, Apr 18, 2012 at 9:01 AM, Juan L. Mateo < juan.mateo@cos.uni-heidelberg.de> wrote: > Hi, > > I don't know which one (or ones) of the new packages is essential because > I installed all of them at once and not one by one to check the result of > trying to update ggbio. > Since this problem could not be reproduced, I guess that it is a specific > misconfiguration of my system but I can't tell which. > > After I run the update command non of my packages were outdated, apart > from ggbio, so everything went fine even for the packages that ggbio 1.0.4 > depends on. > > Best, > Juan > > > On 04/18/2012 05:46 PM, Martin Morgan wrote: > >> On 4/18/2012 8:44 AM, Juan L. Mateo wrote: >> >>> Hi, >>> I came to this problem when I was updating all my bioconductor >>> packages (biocLite(character(), ask=FALSE)) and I had already the >>> previous version of ggbio installed and working. The update was all >>> right but for ggbio. >>> >> >> I guess I'm trying to understand why biocLite didn't update the packages >> that ggbio depends on, and why you had to do that manually? Which >> package was out-of-date after biocLite(character(), ask=FALSE) that >> needed to be updated manually? >> >> Martin >> >>> >>> Best, >>> Juan >>> >>> On 04/18/2012 05:39 PM, Martin Morgan wrote: >>> >>>> On 4/18/2012 5:36 AM, Juan L. Mateo wrote: >>>> >>>>> Hi Vincent, >>>>> >>>>> If I install manually all the packages that are listed in your >>>>> sessionInfo I can install ggbio but with warnings. These warnings >>>>> remain when I load the module. >>>>> >>>> >>>> Did your original attempt to install ggbio indicate that some specific >>>> packages were out of date and need to be updated? biocLite is supposed >>>> to catch these things, so that guessing at which packages are out of >>>> date (via Vince's sessionInfo()!) is not necessary. >>>> >>>> Martin >>>> >>>> Appart from that I have tested several functions of ggbio and they >>>>> seem to work properly. >>>>> >>>>> Thanks for the answer >>>>> Juan >>>>> >>>>> > biocLite("ggbio") >>>>> BioC_mirror: http://bioconductor.org >>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>> Installing package(s) 'ggbio' >>>>> trying URL >>>>> 'http://www.bioconductor.org/**packages/2.10/bioc/src/** >>>>> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz=""> >>>>> ' >>>>> >>>>> >>>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>>> opened URL >>>>> ==============================**==================== >>>>> downloaded 200 Kb >>>>> >>>>> * installing *source* package ‘ggbio’ ... >>>>> ** R >>>>> ** inst >>>>> ** preparing package for lazy loading >>>>> Warning: found methods to import for function ‘as.list’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘IQR’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘NROW’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘aggregate’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘cor’ but not the >>>>> generic itself >>>>> Creating a new generic function for ‘rescale’ in package ‘ggbio’ >>>>> Creating a generic function for ‘summary’ from package ‘base’ in >>>>> package ‘ggbio’ >>>>> Creating a generic function for ‘print’ from package ‘base’ in package >>>>> ‘ggbio’ >>>>> Creating a new generic function for ‘xlim’ in package ‘ggbio’ >>>>> Creating a generic function for ‘update’ from package ‘stats’ in >>>>> package ‘ggbio’ >>>>> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ >>>>> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ >>>>> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ >>>>> Warning in FUN(X[[1L]], ...) : >>>>> Created a package name, ‘2012-04-18 13:53:39’, when none found >>>>> ** help >>>>> *** installing help indices >>>>> ** building package indices >>>>> ** installing vignettes >>>>> ‘intro.Rnw’ >>>>> ** testing if installed package can be loaded >>>>> Warning: found methods to import for function ‘as.list’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘IQR’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘NROW’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘aggregate’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>> generic itself >>>>> Warning: found methods to import for function ‘cor’ but not the >>>>> generic itself >>>>> >>>>> * DONE (ggbio) >>>>> >>>>> The downloaded source packages are in >>>>> ‘/tmp/Rtmp3FIBAU/downloaded_**packages’ >>>>> Warning message: >>>>> installed directory not writable, cannot update packages 'ggbio' >>>>> > library(ggbio) >>>>> Loading required package: ggplot2 >>>>> >>>>> Attaching package: ‘ggbio’ >>>>> >>>>> The following object(s) are masked from ‘package:ggplot2’: >>>>> >>>>> geom_rect, geom_segment, stat_identity, xlim >>>>> >>>>> Warning messages: >>>>> 1: found methods to import for function ‘as.list’ but not the generic >>>>> itself >>>>> 2: found methods to import for function ‘aggregate’ but not the >>>>> generic itself >>>>> 3: found methods to import for function ‘as.table’ but not the generic >>>>> itself >>>>> 4: found methods to import for function ‘complete.cases’ but not the >>>>> generic itself >>>>> 5: found methods to import for function ‘cor’ but not the generic >>>>> itself >>>>> 6: found methods to import for function ‘diff’ but not the generic >>>>> itself >>>>> 7: found methods to import for function ‘drop’ but not the generic >>>>> itself >>>>> 8: found methods to import for function ‘append’ but not the generic >>>>> itself >>>>> 9: found methods to import for function ‘as.data.frame’ but not the >>>>> generic itself >>>>> 10: found methods to import for function ‘as.list’ but not the generic >>>>> itself >>>>> > >>>>> >>>>> >>>>> > sessionInfo() >>>>> R version 2.15.0 (2012-03-30) >>>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=C 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] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>>> [4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.3.6 >>>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>>> [13] digest_0.5.2 GenomicFeatures_1.8.1 GenomicRanges_1.8.3 >>>>> [16] grid_2.15.0 gridExtra_0.9 Hmisc_3.9-3 >>>>> [19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17 >>>>> [22] Matrix_1.0-6 memoise_0.1 munsell_0.3 >>>>> [25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >>>>> [28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.3 >>>>> [31] RSQLite_0.11.1 rtracklayer_1.16.1 scales_0.2.0 >>>>> [34] snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 >>>>> [37] stringr_0.6 survival_2.36-12 tools_2.15.0 >>>>> [40] VariantAnnotation_1.2.5 XML_3.9-4 >>>>> >>>>> >>>>> On 04/18/2012 12:38 PM, Vincent Carey wrote: >>>>> >>>>>> Hi, I am unable to confirm a problem; check your additional resources >>>>>> against the session info below >>>>>> >>>>>> > sessionInfo() >>>>>> R version 2.15.0 Patched (2012-03-31 r58891) >>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C >>>>>> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 >>>>>> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 >>>>>> [7] LC_PAPER=C LC_NAME=C >>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices datasets tools utils methods >>>>>> [8] base >>>>>> >>>>>> other attached packages: >>>>>> [1] ggbio_1.2.8 ggplot2_0.9.0 BiocInstaller_1.4.3 >>>>>> [4] weaver_1.22.0 codetools_0.2-8 digest_0.5.2 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>>>>> [4] biomaRt_2.12.0 Biostrings_2.24.0 biovizBase_1.3.6 >>>>>> [7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >>>>>> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >>>>>> [13] GenomicFeatures_1.8.0 GenomicRanges_1.8.0 grid_2.15.0 >>>>>> [16] gridExtra_0.9 Hmisc_3.9-3 IRanges_1.14.0 >>>>>> [19] lattice_0.20-6 MASS_7.3-17 Matrix_1.0-6 >>>>>> [22] memoise_0.1 munsell_0.3 plyr_1.7.1 >>>>>> [25] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >>>>>> [28] reshape2_1.2.1 Rsamtools_1.8.0 RSQLite_0.11.1 >>>>>> [31] rtracklayer_1.16.0 scales_0.2.0 snpStats_1.6.0 >>>>>> [34] splines_2.15.0 stats4_2.15.0 stringr_0.6 >>>>>> [37] survival_2.36-12 VariantAnnotation_1.2.0 XML_3.9-4 >>>>>> [40] zlibbioc_1.2.0 >>>>>> >>>>>> >>>>>> On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo >>>>>> <juan.mateo@cos.uni-**heidelberg.de<juan.mateo@cos.uni- heidelberg.de=""> >>>>>> <mailto:juan.mateo@cos.uni-**heidelberg.de<juan.mateo@cos.uni- heidelberg.de="">>> >>>>>> wrote: >>>>>> >>>>>> Dear all, >>>>>> >>>>>> I tried to update the package ggbio from version 1.0.4 to the >>>>>> current release version 1.2.8 but there seems to be an error. >>>>>> I list below the error output and sessionInfo(). >>>>>> I tried also to use the development version (1.3.4) but I get the >>>>>> same problem. >>>>>> >>>>>> Best regards >>>>>> >>>>>> >>>>>> > source("http://bioconductor.__**org/biocLite.R >>>>>> <http: bioconductor.org="" **bioclite.r<http:="" bioconductor.org="" b="" ioclite.r=""> >>>>>> >") >>>>>> BiocInstaller version 1.4.3, ?biocLite for help >>>>>> > biocLite("ggbio") >>>>>> BioC_mirror: http://bioconductor.org >>>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>>> Installing package(s) 'ggbio' >>>>>> trying URL >>>>>> 'http://www.bioconductor.org/_**_packages/2.10/bioc/src/__** >>>>>> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" __packag="" es="" 2.10="" bioc="" src="" __contrib="" ggbio_1.2.8.tar.gz=""> >>>>>> >>>>>> >>>>>> <http: www.bioconductor.org="" **packages="" 2.10="" bioc="" src="" **="">>>>>> contrib/ggbio_1.2.8.tar.gz<http: www.bioconductor.org="" packages="" 2.10="" bioc="" src="" contrib="" ggbio_1.2.8.tar.gz=""> >>>>>> >' >>>>>> >>>>>> >>>>>> Content type 'application/x-gzip' length 205262 bytes (200 Kb) >>>>>> opened URL >>>>>> ==============================**__==================== >>>>>> downloaded 200 Kb >>>>>> >>>>>> * installing *source* package ‘ggbio’ ... >>>>>> ** R >>>>>> ** inst >>>>>> ** preparing package for lazy loading >>>>>> Warning: found methods to import for function ‘as.list’ but not the >>>>>> generic itself >>>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>>> generic itself >>>>>> Warning: found methods to import for function ‘IQR’ but not the >>>>>> generic itself >>>>>> Warning: found methods to import for function ‘NROW’ but not the >>>>>> generic itself >>>>>> Warning: found methods to import for function ‘aggregate’ but not >>>>>> the generic itself >>>>>> Warning: found methods to import for function ‘chartr’ but not the >>>>>> generic itself >>>>>> Warning: found methods to import for function ‘cor’ but not the >>>>>> generic itself >>>>>> Creating a new generic function for ‘rescale’ in package ‘ggbio’ >>>>>> Creating a generic function for ‘summary’ from package ‘base’ in >>>>>> package ‘ggbio’ >>>>>> Creating a generic function for ‘print’ from package ‘base’ in >>>>>> package ‘ggbio’ >>>>>> Creating a new generic function for ‘xlim’ in package ‘ggbio’ >>>>>> Creating a generic function for ‘update’ from package ‘stats’ in >>>>>> package ‘ggbio’ >>>>>> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’ >>>>>> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’ >>>>>> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’ >>>>>> Error in conformMethod(signature, mnames, fnames, f, fdef, >>>>>> definition) : >>>>>> in method for ‘autoplot’ with signature ‘x="GRanges"’: formal >>>>>> arguments (x = "GRanges", ... = "GRanges") omitted in the method >>>>>> definition cannot be in the signature >>>>>> Error : unable to load R code in package ‘ggbio’ >>>>>> ERROR: lazy loading failed for package ‘ggbio’ >>>>>> * removing ‘/usr/local/lib/R/site-__**library/ggbio’ >>>>>> * restoring previous ‘/usr/local/lib/R/site-__**library/ggbio’ >>>>>> >>>>>> >>>>>> >>>>>> > sessionInfo() >>>>>> R version 2.15.0 (2012-03-30) >>>>>> Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>>> [7] LC_PAPER=C 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] BiocInstaller_1.4.3 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] tools_2.15.0 >>>>>> >>>>>> >>>>>> -- >>>>>> ============================= >>>>>> Juan L. Mateo PhD. >>>>>> Centre for Organismal Studies (COS) - University of Heidelberg >>>>>> Im Neuenheimer Feld 230 >>>>>> 69120 Heidelberg, Germany >>>>>> Tel: 0049 (0)6221 54 6493 >>>>>> Fax: 0049 (0)6221 54 5639 >>>>>> >>>>>> ______________________________**___________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >>>>>> > >>>>>> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >>>>>> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" s="" tat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>> > >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.__**science.biology.informatics.__** >>>>>> conductor<http: news.gmane.org="" gmane.__science.biology.informa="" tics.__conductor=""> >>>>>> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">>>>>> conductor<http: news.gmane.org="" gmane.science.biology.informati="" cs.conductor=""> >>>>>> > >>>>>> >>>>>> >>>>>> >>>>> ______________________________**_________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.**science.biology.informatics.**cond uctor<http: news.gmane.org="" gmane.science.biology.informatics.conducto="" r=""> >>>>> >>>> >>>> >>>> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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