ggbio::plotIdeogram() not working on R 3.0.2
1
0
Entering edit mode
@lcolladotor
Last seen 5 weeks ago
United States
Dear BioC list and Tengfei Yin, I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 that I think is related to changes in R. The error can also be seen in http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf (search 'unnamed' on the pdf). Below is the error from running the example code for plotIdeogram. library(ggbio) library(biovizBase) data(hg19IdeogramCyto, package = "biovizBase") biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE plotIdeogram(hg19IdeogramCyto, "chr1") ## Error in initialize(value, ...) : unnamed argument must extend either the S3 class or the class of the data part; not true of class “GGbio” traceback() ## 6: stop(gettextf("unnamed argument must extend either the S3 class or the class of the data part; not true of class %s", ## dQuote(Classi)), domain = NA) ## 5: initialize(value, ...) ## 4: initialize(value, ...) ## 3: new("Ideogram", x) ## 2: Ideogram(p) ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") sessionInfo() ## R version 3.0.2 (2013-09-25) ## Platform: x86_64-apple-darwin10.8.0 (64-bit) ## locale: ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## other attached packages: ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 ## loaded via a namespace (and not attached): ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 ## [11] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2 ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 plyr_1.8 ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 ## [36] stringr_0.6.2 tools_3.0.2 VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 ## [41] zlibbioc_1.8.0 Thank you, Leonardo Leonardo Collado Torres, PhD student Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://www.biostat.jhsph.edu/~lcollado/ Blog: http://lcolladotor.github.io/ [[alternative HTML version deleted]]
• 1.6k views
ADD COMMENT •
0
Entering edit mode
Tengfei Yin ▴ 490
@tengfei-yin-6162
Last seen 10.2 years ago
Hi Leonardo, Thanks for reporting the issue, this is probably not R's problem, should be a bug in ggbio's new class, I will look into this. Tengfei On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres <lcollado@jhsph.edu>wrote: > Dear BioC list and Tengfei Yin, > > I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 > that I think is related to changes in R. The error can also be seen in > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf (search > 'unnamed' on the pdf). > > Below is the error from running the example code for plotIdeogram. > > library(ggbio) > library(biovizBase) > data(hg19IdeogramCyto, package = "biovizBase") > biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE > plotIdeogram(hg19IdeogramCyto, "chr1") > > ## Error in initialize(value, ...) : > unnamed argument must extend either the S3 class or the class of the > data part; not true of class “GGbio” > > traceback() > > ## 6: stop(gettextf("unnamed argument must extend either the S3 class or > the class of the data part; not true of class %s", > ## dQuote(Classi)), domain = NA) > ## 5: initialize(value, ...) > ## 4: initialize(value, ...) > ## 3: new("Ideogram", x) > ## 2: Ideogram(p) > ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") > > sessionInfo() > > ## R version 3.0.2 (2013-09-25) > ## Platform: x86_64-apple-darwin10.8.0 (64-bit) > > ## locale: > ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > ## attached base packages: > ## [1] stats graphics grDevices utils datasets methods base > > > ## other attached packages: > ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 > > ## loaded via a namespace (and not attached): > ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 > biomaRt_2.18.0 Biostrings_2.30.0 > ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 > colorspace_1.2-4 DBI_0.2-7 > ## [11] dichromat_2.0-0 digest_0.6.3 > GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 > ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 > IRanges_1.20.4 labeling_0.2 > ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 > parallel_3.0.2 plyr_1.8 > ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 > reshape2_1.2.2 rpart_4.1-3 > ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 > scales_0.2.3 stats4_3.0.2 > ## [36] stringr_0.6.2 tools_3.0.2 > VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 > ## [41] zlibbioc_1.8.0 > > > Thank you, > Leonardo > > Leonardo Collado Torres, PhD student > Department of Biostatistics > Johns Hopkins University > Bloomberg School of Public Health > Website: http://www.biostat.jhsph.edu/~lcollado/ > Blog: http://lcolladotor.github.io/ > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
ADD COMMENT •
0
Entering edit mode
Hi I just fixed this bug in 1.10.1 in release branch, please update one or two days later. Thanks Tengfei On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > Thanks for reporting the issue, this is probably not R's problem, should > be a bug in ggbio's new class, I will look into this. > > Tengfei > > > On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Dear BioC list and Tengfei Yin, >> >> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >> that I think is related to changes in R. The error can also be seen in >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/i nst/doc/ggbio.pdf (search >> 'unnamed' on the pdf). >> >> Below is the error from running the example code for plotIdeogram. >> >> library(ggbio) >> library(biovizBase) >> data(hg19IdeogramCyto, package = "biovizBase") >> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >> plotIdeogram(hg19IdeogramCyto, "chr1") >> >> ## Error in initialize(value, ...) : >> unnamed argument must extend either the S3 class or the class of the >> data part; not true of class “GGbio” >> >> traceback() >> >> ## 6: stop(gettextf("unnamed argument must extend either the S3 class or >> the class of the data part; not true of class %s", >> ## dQuote(Classi)), domain = NA) >> ## 5: initialize(value, ...) >> ## 4: initialize(value, ...) >> ## 3: new("Ideogram", x) >> ## 2: Ideogram(p) >> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >> >> sessionInfo() >> >> ## R version 3.0.2 (2013-09-25) >> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> ## locale: >> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> ## attached base packages: >> ## [1] stats graphics grDevices utils datasets methods base >> >> >> ## other attached packages: >> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >> >> ## loaded via a namespace (and not attached): >> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >> colorspace_1.2-4 DBI_0.2-7 >> ## [11] dichromat_2.0-0 digest_0.6.3 >> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >> IRanges_1.20.4 labeling_0.2 >> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >> parallel_3.0.2 plyr_1.8 >> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> reshape2_1.2.2 rpart_4.1-3 >> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >> ## [36] stringr_0.6.2 tools_3.0.2 >> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >> ## [41] zlibbioc_1.8.0 >> >> >> Thank you, >> Leonardo >> >> Leonardo Collado Torres, PhD student >> Department of Biostatistics >> Johns Hopkins University >> Bloomberg School of Public Health >> Website: http://www.biostat.jhsph.edu/~lcollado/ >> Blog: http://lcolladotor.github.io/ >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Thank you very much Tengfei! On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi > > I just fixed this bug in 1.10.1 in release branch, please update one or > two days later. > > Thanks > > Tengfei > > > On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi Leonardo, >> >> Thanks for reporting the issue, this is probably not R's problem, should >> be a bug in ggbio's new class, I will look into this. >> >> Tengfei >> >> >> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Dear BioC list and Tengfei Yin, >>> >>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >>> that I think is related to changes in R. The error can also be seen in >>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ inst/doc/ggbio.pdf (search >>> 'unnamed' on the pdf). >>> >>> Below is the error from running the example code for plotIdeogram. >>> >>> library(ggbio) >>> library(biovizBase) >>> data(hg19IdeogramCyto, package = "biovizBase") >>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>> plotIdeogram(hg19IdeogramCyto, "chr1") >>> >>> ## Error in initialize(value, ...) : >>> unnamed argument must extend either the S3 class or the class of the >>> data part; not true of class “GGbio” >>> >>> traceback() >>> >>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class or >>> the class of the data part; not true of class %s", >>> ## dQuote(Classi)), domain = NA) >>> ## 5: initialize(value, ...) >>> ## 4: initialize(value, ...) >>> ## 3: new("Ideogram", x) >>> ## 2: Ideogram(p) >>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>> >>> sessionInfo() >>> >>> ## R version 3.0.2 (2013-09-25) >>> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> ## locale: >>> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> ## attached base packages: >>> ## [1] stats graphics grDevices utils datasets methods base >>> >>> >>> ## other attached packages: >>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>> >>> ## loaded via a namespace (and not attached): >>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >>> colorspace_1.2-4 DBI_0.2-7 >>> ## [11] dichromat_2.0-0 digest_0.6.3 >>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>> IRanges_1.20.4 labeling_0.2 >>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>> parallel_3.0.2 plyr_1.8 >>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>> reshape2_1.2.2 rpart_4.1-3 >>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>> ## [36] stringr_0.6.2 tools_3.0.2 >>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>> ## [41] zlibbioc_1.8.0 >>> >>> >>> Thank you, >>> Leonardo >>> >>> Leonardo Collado Torres, PhD student >>> Department of Biostatistics >>> Johns Hopkins University >>> Bloomberg School of Public Health >>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>> Blog: http://lcolladotor.github.io/ >>> >> >> >> >> -- >> Tengfei Yin, PhD >> Seven Bridges Genomics >> sbgenomics.com >> 625 Mt. Auburn St. Suite #208 >> Cambridge, MA 02138 >> (617) 866-0446 >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Hi Tengfei, Sadly, I am currently having the same issue with version 1.10.7 from the release branch. Also, http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf compiled on Nov 14th has the same issue as expected (R session at the end shows that it was compiled with version 1.10.7). The devel branch http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/doc/g gbio.pdf from Nov 14th does have a working plotIdeogram(). In our local R-devel version, I cannot load ggbio due to namespace errors. Note that this R-devel version is from Nov 15th, so maybe some changes were introduced to Rsamtools that day that broke things in ggbio. Best, Leonardo ### Session information using version 1.10.7 where the example of plotIdeogram() fails > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 ggplot2_0.9.3.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 stringr_0.6.2 [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 XVector_0.2.0 zlibbioc_1.8.0 #### Session information using local R-devel $ R-devel R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered Consequences" [removed other info] > library(ggbio) Loading required package: ggplot2 No methods found in "Rsamtools" for requests: readGAlignmentsFromBam Error : object 'readGAlignmentsFromBam' is not exported by 'namespace:Rsamtools' Error: package or namespace load failed for 'ggbio' > sessionInfo() R Under development (unstable) (2013-11-15 r64218) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] ggplot2_0.9.3.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 [13] digest_0.6.3 GenomicAlignments_0.99.2 GenomicFeatures_1.15.2 [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 > On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > Thank you very much Tengfei! > > > On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi >> >> I just fixed this bug in 1.10.1 in release branch, please update one or >> two days later. >> >> Thanks >> >> Tengfei >> >> >> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: >> >>> Hi Leonardo, >>> >>> Thanks for reporting the issue, this is probably not R's problem, should >>> be a bug in ggbio's new class, I will look into this. >>> >>> Tengfei >>> >>> >>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>> lcollado@jhsph.edu> wrote: >>> >>>> Dear BioC list and Tengfei Yin, >>>> >>>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >>>> that I think is related to changes in R. The error can also be seen in >>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio /inst/doc/ggbio.pdf (search >>>> 'unnamed' on the pdf). >>>> >>>> Below is the error from running the example code for plotIdeogram. >>>> >>>> library(ggbio) >>>> library(biovizBase) >>>> data(hg19IdeogramCyto, package = "biovizBase") >>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>> >>>> ## Error in initialize(value, ...) : >>>> unnamed argument must extend either the S3 class or the class of the >>>> data part; not true of class “GGbio” >>>> >>>> traceback() >>>> >>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class >>>> or the class of the data part; not true of class %s", >>>> ## dQuote(Classi)), domain = NA) >>>> ## 5: initialize(value, ...) >>>> ## 4: initialize(value, ...) >>>> ## 3: new("Ideogram", x) >>>> ## 2: Ideogram(p) >>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>> >>>> sessionInfo() >>>> >>>> ## R version 3.0.2 (2013-09-25) >>>> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>> >>>> ## locale: >>>> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> ## attached base packages: >>>> ## [1] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> ## other attached packages: >>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>> >>>> ## loaded via a namespace (and not attached): >>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >>>> colorspace_1.2-4 DBI_0.2-7 >>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>> IRanges_1.20.4 labeling_0.2 >>>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>>> parallel_3.0.2 plyr_1.8 >>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>>> reshape2_1.2.2 rpart_4.1-3 >>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>> ## [41] zlibbioc_1.8.0 >>>> >>>> >>>> Thank you, >>>> Leonardo >>>> >>>> Leonardo Collado Torres, PhD student >>>> Department of Biostatistics >>>> Johns Hopkins University >>>> Bloomberg School of Public Health >>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>> Blog: http://lcolladotor.github.io/ >>>> >>> >>> >>> >>> -- >>> Tengfei Yin, PhD >>> Seven Bridges Genomics >>> sbgenomics.com >>> 625 Mt. Auburn St. Suite #208 >>> Cambridge, MA 02138 >>> (617) 866-0446 >>> >> >> >> >> -- >> Tengfei Yin, PhD >> Seven Bridges Genomics >> sbgenomics.com >> 625 Mt. Auburn St. Suite #208 >> Cambridge, MA 02138 >> (617) 866-0446 >> > > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Hi Leonardo, Thanks for your feedback. It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the reason I updated the GGbio class and default ggplot() method, I just fixed it in released branch 1.10.8. I will work on the devel branch problem you reported. cheers Tengfei On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < lcollado@jhsph.edu> wrote: > Hi Tengfei, > > Sadly, I am currently having the same issue with version 1.10.7 from the > release branch. Also, > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf compiled > on Nov 14th has the same issue as expected (R session at the end shows that > it was compiled with version 1.10.7). The devel branch > http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/doc /ggbio.pdf from > Nov 14th does have a working plotIdeogram(). > > In our local R-devel version, I cannot load ggbio due to namespace errors. > Note that this R-devel version is from Nov 15th, so maybe some changes were > introduced to Rsamtools that day that broke things in ggbio. > > Best, > Leonardo > > > > ### Session information using version 1.10.7 where the example of > plotIdeogram() fails > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 > ggplot2_0.9.3.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 > biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 > [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 > DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 > [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 > gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 > [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 > MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 > [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 > RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 > [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 > scales_0.2.3 stats4_3.0.2 stringr_0.6.2 > [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 > XVector_0.2.0 zlibbioc_1.8.0 > > > #### Session information using local R-devel > > $ R-devel > > R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered > Consequences" > > [removed other info] > > > library(ggbio) > Loading required package: ggplot2 > No methods found in "Rsamtools" for requests: readGAlignmentsFromBam > Error : object 'readGAlignmentsFromBam' is not exported by > 'namespace:Rsamtools' > Error: package or namespace load failed for 'ggbio' > > sessionInfo() > R Under development (unstable) (2013-11-15 r64218) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=en_US.iso885915 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] ggplot2_0.9.3.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 > [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 > [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 > [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 > [13] digest_0.6.3 GenomicAlignments_0.99.2 > GenomicFeatures_1.15.2 > [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 > [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 > [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 > [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 > [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 > [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 > [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 > [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 > > > > > > On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Thank you very much Tengfei! >> >> >> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>> > wrote: >> >>> Hi >>> >>> I just fixed this bug in 1.10.1 in release branch, please update one or >>> two days later. >>> >>> Thanks >>> >>> Tengfei >>> >>> >>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: >>> >>>> Hi Leonardo, >>>> >>>> Thanks for reporting the issue, this is probably not R's problem, >>>> should be a bug in ggbio's new class, I will look into this. >>>> >>>> Tengfei >>>> >>>> >>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>> lcollado@jhsph.edu> wrote: >>>> >>>>> Dear BioC list and Tengfei Yin, >>>>> >>>>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >>>>> that I think is related to changes in R. The error can also be seen in >>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbi o/inst/doc/ggbio.pdf (search >>>>> 'unnamed' on the pdf). >>>>> >>>>> Below is the error from running the example code for plotIdeogram. >>>>> >>>>> library(ggbio) >>>>> library(biovizBase) >>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>> >>>>> ## Error in initialize(value, ...) : >>>>> unnamed argument must extend either the S3 class or the class of the >>>>> data part; not true of class “GGbio” >>>>> >>>>> traceback() >>>>> >>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class >>>>> or the class of the data part; not true of class %s", >>>>> ## dQuote(Classi)), domain = NA) >>>>> ## 5: initialize(value, ...) >>>>> ## 4: initialize(value, ...) >>>>> ## 3: new("Ideogram", x) >>>>> ## 2: Ideogram(p) >>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>> >>>>> sessionInfo() >>>>> >>>>> ## R version 3.0.2 (2013-09-25) >>>>> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>>> >>>>> ## locale: >>>>> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>> >>>>> ## attached base packages: >>>>> ## [1] stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> ## other attached packages: >>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>> >>>>> ## loaded via a namespace (and not attached): >>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >>>>> colorspace_1.2-4 DBI_0.2-7 >>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>>> IRanges_1.20.4 labeling_0.2 >>>>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>>>> parallel_3.0.2 plyr_1.8 >>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>>>> reshape2_1.2.2 rpart_4.1-3 >>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>> ## [41] zlibbioc_1.8.0 >>>>> >>>>> >>>>> Thank you, >>>>> Leonardo >>>>> >>>>> Leonardo Collado Torres, PhD student >>>>> Department of Biostatistics >>>>> Johns Hopkins University >>>>> Bloomberg School of Public Health >>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>> Blog: http://lcolladotor.github.io/ >>>>> >>>> >>>> >>>> >>>> -- >>>> Tengfei Yin, PhD >>>> Seven Bridges Genomics >>>> sbgenomics.com >>>> 625 Mt. Auburn St. Suite #208 >>>> Cambridge, MA 02138 >>>> (617) 866-0446 >>>> >>> >>> >>> >>> -- >>> Tengfei Yin, PhD >>> Seven Bridges Genomics >>> sbgenomics.com >>> 625 Mt. Auburn St. Suite #208 >>> Cambridge, MA 02138 >>> (617) 866-0446 >>> >> >> > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Thank you for the speedy fix Tengfei! As for the devel branch problem, I think that in Rsamtools 1.14.1 readGAlignmentsFromBam was exported but in version Rsamtools_1.15.7 that is no longer the case since this function is now in GenomicAlignments::readGAlignments Cheers, Leo On Wed, Nov 20, 2013 at 1:43 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > Thanks for your feedback. > > It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the reason > I updated the GGbio class and default ggplot() method, I just fixed it in > released branch 1.10.8. I will work on the devel branch problem you > reported. > > cheers > > Tengfei > > > On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Hi Tengfei, >> >> Sadly, I am currently having the same issue with version 1.10.7 from the >> release branch. Also, >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/i nst/doc/ggbio.pdf compiled >> on Nov 14th has the same issue as expected (R session at the end shows that >> it was compiled with version 1.10.7). The devel branch >> http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/do c/ggbio.pdf from >> Nov 14th does have a working plotIdeogram(). >> >> In our local R-devel version, I cannot load ggbio due to namespace >> errors. Note that this R-devel version is from Nov 15th, so maybe some >> changes were introduced to Rsamtools that day that broke things in ggbio. >> >> Best, >> Leonardo >> >> >> >> ### Session information using version 1.10.7 where the example of >> plotIdeogram() fails >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 >> ggplot2_0.9.3.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 >> biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >> [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 >> DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 >> [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >> [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 >> MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 >> [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >> [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >> [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 >> XVector_0.2.0 zlibbioc_1.8.0 >> >> >> #### Session information using local R-devel >> >> $ R-devel >> >> R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered >> Consequences" >> >> [removed other info] >> >> > library(ggbio) >> Loading required package: ggplot2 >> No methods found in "Rsamtools" for requests: readGAlignmentsFromBam >> Error : object 'readGAlignmentsFromBam' is not exported by >> 'namespace:Rsamtools' >> Error: package or namespace load failed for 'ggbio' >> > sessionInfo() >> R Under development (unstable) (2013-11-15 r64218) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] ggplot2_0.9.3.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 >> [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 >> [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 >> [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >> [13] digest_0.6.3 GenomicAlignments_0.99.2 >> GenomicFeatures_1.15.2 >> [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 >> [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 >> [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 >> [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 >> [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 >> [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 >> [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >> [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 >> > >> >> >> >> On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Thank you very much Tengfei! >>> >>> >>> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin < >>> tengfei.yin@sbgenomics.com> wrote: >>> >>>> Hi >>>> >>>> I just fixed this bug in 1.10.1 in release branch, please update one or >>>> two days later. >>>> >>>> Thanks >>>> >>>> Tengfei >>>> >>>> >>>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>>>> > wrote: >>>> >>>>> Hi Leonardo, >>>>> >>>>> Thanks for reporting the issue, this is probably not R's problem, >>>>> should be a bug in ggbio's new class, I will look into this. >>>>> >>>>> Tengfei >>>>> >>>>> >>>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>>> lcollado@jhsph.edu> wrote: >>>>> >>>>>> Dear BioC list and Tengfei Yin, >>>>>> >>>>>> I am encountering an error when using ggbio::plotIdeogram() on R >>>>>> 3.0.2 that I think is related to changes in R. The error can also be seen >>>>>> in >>>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggb io/inst/doc/ggbio.pdf (search >>>>>> 'unnamed' on the pdf). >>>>>> >>>>>> Below is the error from running the example code for plotIdeogram. >>>>>> >>>>>> library(ggbio) >>>>>> library(biovizBase) >>>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>> >>>>>> ## Error in initialize(value, ...) : >>>>>> unnamed argument must extend either the S3 class or the class of >>>>>> the data part; not true of class “GGbio” >>>>>> >>>>>> traceback() >>>>>> >>>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class >>>>>> or the class of the data part; not true of class %s", >>>>>> ## dQuote(Classi)), domain = NA) >>>>>> ## 5: initialize(value, ...) >>>>>> ## 4: initialize(value, ...) >>>>>> ## 3: new("Ideogram", x) >>>>>> ## 2: Ideogram(p) >>>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>> >>>>>> sessionInfo() >>>>>> >>>>>> ## R version 3.0.2 (2013-09-25) >>>>>> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>>>> >>>>>> ## locale: >>>>>> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>> >>>>>> ## attached base packages: >>>>>> ## [1] stats graphics grDevices utils datasets methods >>>>>> base >>>>>> >>>>>> ## other attached packages: >>>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>>> >>>>>> ## loaded via a namespace (and not attached): >>>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 >>>>>> cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>>>> IRanges_1.20.4 labeling_0.2 >>>>>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>>>>> parallel_3.0.2 plyr_1.8 >>>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 >>>>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>>> ## [41] zlibbioc_1.8.0 >>>>>> >>>>>> >>>>>> Thank you, >>>>>> Leonardo >>>>>> >>>>>> Leonardo Collado Torres, PhD student >>>>>> Department of Biostatistics >>>>>> Johns Hopkins University >>>>>> Bloomberg School of Public Health >>>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>>> Blog: http://lcolladotor.github.io/ >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Tengfei Yin, PhD >>>>> Seven Bridges Genomics >>>>> sbgenomics.com >>>>> 625 Mt. Auburn St. Suite #208 >>>>> Cambridge, MA 02138 >>>>> (617) 866-0446 >>>>> >>>> >>>> >>>> >>>> -- >>>> Tengfei Yin, PhD >>>> Seven Bridges Genomics >>>> sbgenomics.com >>>> 625 Mt. Auburn St. Suite #208 >>>> Cambridge, MA 02138 >>>> (617) 866-0446 >>>> >>> >>> >> > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Hi Leonardo, I think some of the package on your R-devel are our of date, would you please run source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") or biocLite() to update packages You will probably get a new error message, because of affyPLM in devel branch, then update ggbio-devel one day later will fix that. Thanks Tengfei On Wed, Nov 20, 2013 at 2:03 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > Thank you for the speedy fix Tengfei! > > As for the devel branch problem, I think that in Rsamtools > 1.14.1 readGAlignmentsFromBam was exported but in version Rsamtools_1.15.7 > that is no longer the case since this function is now > in GenomicAlignments::readGAlignments > > Cheers, > Leo > > > On Wed, Nov 20, 2013 at 1:43 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi Leonardo, >> >> Thanks for your feedback. >> >> It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the reason >> I updated the GGbio class and default ggplot() method, I just fixed it in >> released branch 1.10.8. I will work on the devel branch problem you >> reported. >> >> cheers >> >> Tengfei >> >> >> On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Hi Tengfei, >>> >>> Sadly, I am currently having the same issue with version 1.10.7 from the >>> release branch. Also, >>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ inst/doc/ggbio.pdf compiled >>> on Nov 14th has the same issue as expected (R session at the end shows that >>> it was compiled with version 1.10.7). The devel branch >>> http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/d oc/ggbio.pdf from >>> Nov 14th does have a working plotIdeogram(). >>> >>> In our local R-devel version, I cannot load ggbio due to namespace >>> errors. Note that this R-devel version is from Nov 15th, so maybe some >>> changes were introduced to Rsamtools that day that broke things in ggbio. >>> >>> Best, >>> Leonardo >>> >>> >>> >>> ### Session information using version 1.10.7 where the example of >>> plotIdeogram() fails >>> >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 >>> ggplot2_0.9.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 >>> biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >>> [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 >>> DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 >>> [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>> [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 >>> MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 >>> [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>> [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >>> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >>> [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 >>> XVector_0.2.0 zlibbioc_1.8.0 >>> >>> >>> #### Session information using local R-devel >>> >>> $ R-devel >>> >>> R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered >>> Consequences" >>> >>> [removed other info] >>> >>> > library(ggbio) >>> Loading required package: ggplot2 >>> No methods found in "Rsamtools" for requests: readGAlignmentsFromBam >>> Error : object 'readGAlignmentsFromBam' is not exported by >>> 'namespace:Rsamtools' >>> Error: package or namespace load failed for 'ggbio' >>> > sessionInfo() >>> R Under development (unstable) (2013-11-15 r64218) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >>> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets utils methods base >>> >>> other attached packages: >>> [1] ggplot2_0.9.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 >>> [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 >>> [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 >>> [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >>> [13] digest_0.6.3 GenomicAlignments_0.99.2 >>> GenomicFeatures_1.15.2 >>> [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 >>> [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 >>> [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 >>> [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 >>> [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>> [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 >>> [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 >>> [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >>> [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 >>> > >>> >>> >>> >>> On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < >>> lcollado@jhsph.edu> wrote: >>> >>>> Thank you very much Tengfei! >>>> >>>> >>>> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin < >>>> tengfei.yin@sbgenomics.com> wrote: >>>> >>>>> Hi >>>>> >>>>> I just fixed this bug in 1.10.1 in release branch, please update one >>>>> or two days later. >>>>> >>>>> Thanks >>>>> >>>>> Tengfei >>>>> >>>>> >>>>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin < >>>>> tengfei.yin@sbgenomics.com> wrote: >>>>> >>>>>> Hi Leonardo, >>>>>> >>>>>> Thanks for reporting the issue, this is probably not R's problem, >>>>>> should be a bug in ggbio's new class, I will look into this. >>>>>> >>>>>> Tengfei >>>>>> >>>>>> >>>>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>>>> lcollado@jhsph.edu> wrote: >>>>>> >>>>>>> Dear BioC list and Tengfei Yin, >>>>>>> >>>>>>> I am encountering an error when using ggbio::plotIdeogram() on R >>>>>>> 3.0.2 that I think is related to changes in R. The error can also be seen >>>>>>> in >>>>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/gg bio/inst/doc/ggbio.pdf (search >>>>>>> 'unnamed' on the pdf). >>>>>>> >>>>>>> Below is the error from running the example code for plotIdeogram. >>>>>>> >>>>>>> library(ggbio) >>>>>>> library(biovizBase) >>>>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>> >>>>>>> ## Error in initialize(value, ...) : >>>>>>> unnamed argument must extend either the S3 class or the class of >>>>>>> the data part; not true of class “GGbio” >>>>>>> >>>>>>> traceback() >>>>>>> >>>>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 >>>>>>> class or the class of the data part; not true of class %s", >>>>>>> ## dQuote(Classi)), domain = NA) >>>>>>> ## 5: initialize(value, ...) >>>>>>> ## 4: initialize(value, ...) >>>>>>> ## 3: new("Ideogram", x) >>>>>>> ## 2: Ideogram(p) >>>>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>> >>>>>>> sessionInfo() >>>>>>> >>>>>>> ## R version 3.0.2 (2013-09-25) >>>>>>> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>>>>> >>>>>>> ## locale: >>>>>>> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>>> >>>>>>> ## attached base packages: >>>>>>> ## [1] stats graphics grDevices utils datasets methods >>>>>>> base >>>>>>> >>>>>>> ## other attached packages: >>>>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>>>> >>>>>>> ## loaded via a namespace (and not attached): >>>>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 >>>>>>> cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>>>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>>>>> IRanges_1.20.4 labeling_0.2 >>>>>>> ## [21] lattice_0.20-24 MASS_7.3-29 >>>>>>> munsell_0.4.2 parallel_3.0.2 plyr_1.8 >>>>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 >>>>>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>>>> ## [41] zlibbioc_1.8.0 >>>>>>> >>>>>>> >>>>>>> Thank you, >>>>>>> Leonardo >>>>>>> >>>>>>> Leonardo Collado Torres, PhD student >>>>>>> Department of Biostatistics >>>>>>> Johns Hopkins University >>>>>>> Bloomberg School of Public Health >>>>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>>>> Blog: http://lcolladotor.github.io/ >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Tengfei Yin, PhD >>>>>> Seven Bridges Genomics >>>>>> sbgenomics.com >>>>>> 625 Mt. Auburn St. Suite #208 >>>>>> Cambridge, MA 02138 >>>>>> (617) 866-0446 >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Tengfei Yin, PhD >>>>> Seven Bridges Genomics >>>>> sbgenomics.com >>>>> 625 Mt. Auburn St. Suite #208 >>>>> Cambridge, MA 02138 >>>>> (617) 866-0446 >>>>> >>>> >>>> >>> >> >> >> -- >> Tengfei Yin, PhD >> Seven Bridges Genomics >> sbgenomics.com >> 625 Mt. Auburn St. Suite #208 >> Cambridge, MA 02138 >> (617) 866-0446 >> > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Hi Tengfei, After updating the packages on our R-devel I was able to load ggbio as you stated. Thanks, Leo On Wed, Nov 20, 2013 at 4:13 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > I think some of the package on your R-devel are our of date, would you > please run > > source("http://bioconductor.org/biocLite.R") > biocLite("BiocUpgrade") > > or biocLite() to update packages > > You will probably get a new error message, because of affyPLM in devel > branch, then update ggbio-devel one day later will fix that. > > Thanks > > Tengfei > > > On Wed, Nov 20, 2013 at 2:03 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Thank you for the speedy fix Tengfei! >> >> As for the devel branch problem, I think that in Rsamtools >> 1.14.1 readGAlignmentsFromBam was exported but in version Rsamtools_1.15.7 >> that is no longer the case since this function is now >> in GenomicAlignments::readGAlignments >> >> Cheers, >> Leo >> >> >> On Wed, Nov 20, 2013 at 1:43 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: >> >>> Hi Leonardo, >>> >>> Thanks for your feedback. >>> >>> It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the >>> reason I updated the GGbio class and default ggplot() method, I just fixed >>> it in released branch 1.10.8. I will work on the devel branch problem you >>> reported. >>> >>> cheers >>> >>> Tengfei >>> >>> >>> On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < >>> lcollado@jhsph.edu> wrote: >>> >>>> Hi Tengfei, >>>> >>>> Sadly, I am currently having the same issue with version 1.10.7 from >>>> the release branch. Also, >>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio /inst/doc/ggbio.pdf compiled >>>> on Nov 14th has the same issue as expected (R session at the end shows that >>>> it was compiled with version 1.10.7). The devel branch >>>> http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/ doc/ggbio.pdf from >>>> Nov 14th does have a working plotIdeogram(). >>>> >>>> In our local R-devel version, I cannot load ggbio due to namespace >>>> errors. Note that this R-devel version is from Nov 15th, so maybe some >>>> changes were introduced to Rsamtools that day that broke things in ggbio. >>>> >>>> Best, >>>> Leonardo >>>> >>>> >>>> >>>> ### Session information using version 1.10.7 where the example of >>>> plotIdeogram() fails >>>> >>>> > sessionInfo() >>>> R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> other attached packages: >>>> [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 >>>> ggplot2_0.9.3.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 >>>> biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >>>> [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 >>>> DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 >>>> [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>> [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 >>>> MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 >>>> >>>> [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>> [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >>>> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >>>> [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 >>>> XVector_0.2.0 zlibbioc_1.8.0 >>>> >>>> >>>> #### Session information using local R-devel >>>> >>>> $ R-devel >>>> >>>> R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered >>>> Consequences" >>>> >>>> [removed other info] >>>> >>>> > library(ggbio) >>>> Loading required package: ggplot2 >>>> No methods found in "Rsamtools" for requests: readGAlignmentsFromBam >>>> Error : object 'readGAlignmentsFromBam' is not exported by >>>> 'namespace:Rsamtools' >>>> Error: package or namespace load failed for 'ggbio' >>>> > sessionInfo() >>>> R Under development (unstable) (2013-11-15 r64218) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >>>> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >>>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices datasets utils methods base >>>> >>>> other attached packages: >>>> [1] ggplot2_0.9.3.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.25.3 Biobase_2.23.3 >>>> BiocGenerics_0.9.0 >>>> [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 >>>> [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 >>>> [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >>>> [13] digest_0.6.3 GenomicAlignments_0.99.2 >>>> GenomicFeatures_1.15.2 >>>> [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 >>>> [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 >>>> [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 >>>> [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 >>>> [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>>> [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 >>>> [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 >>>> [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >>>> [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 >>>> > >>>> >>>> >>>> >>>> On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < >>>> lcollado@jhsph.edu> wrote: >>>> >>>>> Thank you very much Tengfei! >>>>> >>>>> >>>>> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin < >>>>> tengfei.yin@sbgenomics.com> wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> I just fixed this bug in 1.10.1 in release branch, please update one >>>>>> or two days later. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Tengfei >>>>>> >>>>>> >>>>>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin < >>>>>> tengfei.yin@sbgenomics.com> wrote: >>>>>> >>>>>>> Hi Leonardo, >>>>>>> >>>>>>> Thanks for reporting the issue, this is probably not R's problem, >>>>>>> should be a bug in ggbio's new class, I will look into this. >>>>>>> >>>>>>> Tengfei >>>>>>> >>>>>>> >>>>>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>>>>> lcollado@jhsph.edu> wrote: >>>>>>> >>>>>>>> Dear BioC list and Tengfei Yin, >>>>>>>> >>>>>>>> I am encountering an error when using ggbio::plotIdeogram() on R >>>>>>>> 3.0.2 that I think is related to changes in R. The error can also be seen >>>>>>>> in >>>>>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/g gbio/inst/doc/ggbio.pdf (search >>>>>>>> 'unnamed' on the pdf). >>>>>>>> >>>>>>>> Below is the error from running the example code for plotIdeogram. >>>>>>>> >>>>>>>> library(ggbio) >>>>>>>> library(biovizBase) >>>>>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>>> >>>>>>>> ## Error in initialize(value, ...) : >>>>>>>> unnamed argument must extend either the S3 class or the class of >>>>>>>> the data part; not true of class “GGbio” >>>>>>>> >>>>>>>> traceback() >>>>>>>> >>>>>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 >>>>>>>> class or the class of the data part; not true of class %s", >>>>>>>> ## dQuote(Classi)), domain = NA) >>>>>>>> ## 5: initialize(value, ...) >>>>>>>> ## 4: initialize(value, ...) >>>>>>>> ## 3: new("Ideogram", x) >>>>>>>> ## 2: Ideogram(p) >>>>>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>>> >>>>>>>> sessionInfo() >>>>>>>> >>>>>>>> ## R version 3.0.2 (2013-09-25) >>>>>>>> ## Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>>>>>> >>>>>>>> ## locale: >>>>>>>> ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>> >>>>>>>> ## attached base packages: >>>>>>>> ## [1] stats graphics grDevices utils datasets methods >>>>>>>> base >>>>>>>> >>>>>>>> ## other attached packages: >>>>>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>>>>> >>>>>>>> ## loaded via a namespace (and not attached): >>>>>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 >>>>>>>> cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>>>>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 >>>>>>>> Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2 >>>>>>>> ## [21] lattice_0.20-24 MASS_7.3-29 >>>>>>>> munsell_0.4.2 parallel_3.0.2 plyr_1.8 >>>>>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 >>>>>>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>>>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>>>>> ## [41] zlibbioc_1.8.0 >>>>>>>> >>>>>>>> >>>>>>>> Thank you, >>>>>>>> Leonardo >>>>>>>> >>>>>>>> Leonardo Collado Torres, PhD student >>>>>>>> Department of Biostatistics >>>>>>>> Johns Hopkins University >>>>>>>> Bloomberg School of Public Health >>>>>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>>>>> Blog: http://lcolladotor.github.io/ >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Tengfei Yin, PhD >>>>>>> Seven Bridges Genomics >>>>>>> sbgenomics.com >>>>>>> 625 Mt. Auburn St. Suite #208 >>>>>>> Cambridge, MA 02138 >>>>>>> (617) 866-0446 >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Tengfei Yin, PhD >>>>>> Seven Bridges Genomics >>>>>> sbgenomics.com >>>>>> 625 Mt. Auburn St. Suite #208 >>>>>> Cambridge, MA 02138 >>>>>> (617) 866-0446 >>>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> Tengfei Yin, PhD >>> Seven Bridges Genomics >>> sbgenomics.com >>> 625 Mt. Auburn St. Suite #208 >>> Cambridge, MA 02138 >>> (617) 866-0446 >>> >> >> > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > [[alternative HTML version deleted]]
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 707 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6