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lawremi / ggbio

Grid and ggplot2 based visualization for biological data
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autoplot error #33

Open huwind opened 11 years ago

huwind commented 11 years ago

First time to try autoplot after the installation. I followed the examples to get started, step by step.

autoplot(gr) Error in rep.int("", ncol(r)) : incorrect type for second argument

R version 2.15.2. Thanks for any tips!

tengfei commented 11 years ago

Hi

Would you mind run sessionInfo()? this error is probably caused by package version difference.

Thanks

Tengfei

On Thu, Apr 11, 2013 at 10:53 AM, huwind notifications@github.com wrote:

First time to try autoplot after the installation. I followed the examples to get started, step by step.

autoplot(gr) Error in rep.int("", ncol(r)) : incorrect type for second argument

R version 2.15.2. Thanks for any tips!

— Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/33 .

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274

huwind commented 11 years ago

sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-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] grid stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] CNAnorm_1.2.0 DNAcopy_1.30.0 [3] GenomicRanges_1.8.13 IRanges_1.14.4 [5] ggbio_1.4.6 BiocInstaller_1.4.9 [7] SplicingCompass_1.0 mclust_4.0 [9] VennDiagram_1.5.1 lumiHumanIDMapping_1.10.0 [11] annotate_1.34.1 gplots_2.11.0 [13] MASS_7.3-22 KernSmooth_2.23-8 [15] caTools_1.14 gdata_2.12.0 [17] gtools_2.7.0 limma_3.12.3 [19] lumiHumanAll.db_1.18.0 org.Hs.eg.db_2.7.1 [21] RSQLite_0.11.2 DBI_0.2-5 [23] AnnotationDbi_1.18.4 lumi_2.8.0 [25] nleqslv_2.0 methylumi_2.2.0 [27] ggplot2_0.9.3.1 reshape2_1.2.2 [29] scales_0.2.3 Biobase_2.16.0 [31] BiocGenerics_0.2.0

loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 bigmemory_4.4.3 [4] bigmemory.sri_0.1.2 biomaRt_2.12.0 Biostrings_2.24.1 [7] biovizBase_1.4.2 bitops_1.0-5 BSgenome_1.24.0 [10] cluster_1.14.3 colorspace_1.2-0 dichromat_2.0-0 [13] digest_0.5.2 GenomicFeatures_1.8.3 genoset_1.6.0 [16] gridExtra_0.9.1 gtable_0.1.2 hdrcde_2.16 [19] Hmisc_3.9-3 labeling_0.1 lattice_0.20-10 [22] Matrix_1.0-9 mgcv_1.7-22 munsell_0.4 [25] nlme_3.1-105 plyr_1.7.1 preprocessCore_1.18.0 [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-3 [31] Rsamtools_1.8.6 rtracklayer_1.16.3 snpStats_1.6.0 [34] splines_2.15.2 stats4_2.15.2 stringr_0.6.1 [37] survival_2.36-14 tools_2.15.2 VariantAnnotation_1.2.11 [40] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.2.0

On Thu, Apr 11, 2013 at 12:53 PM, Tengfei Yin notifications@github.comwrote:

Hi

Would you mind run sessionInfo()? this error is probably caused by package version difference.

Thanks

Tengfei

On Thu, Apr 11, 2013 at 10:53 AM, huwind notifications@github.com wrote:

First time to try autoplot after the installation. I followed the examples to get started, step by step.

autoplot(gr) Error in rep.int("", ncol(r)) : incorrect type for second argument

R version 2.15.2. Thanks for any tips!

— Reply to this email directly or view it on GitHub< https://github.com/tengfei/ggbio/issues/33> .

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274

— Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/33#issuecomment-16247158 .

tengfei commented 11 years ago

would you mind try

source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") biocLite()

to update packages and run the example again?

Tengfei

On Thu, Apr 11, 2013 at 11:59 AM, huwind notifications@github.com wrote:

sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-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] grid stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] CNAnorm_1.2.0 DNAcopy_1.30.0 [3] GenomicRanges_1.8.13 IRanges_1.14.4 [5] ggbio_1.4.6 BiocInstaller_1.4.9 [7] SplicingCompass_1.0 mclust_4.0 [9] VennDiagram_1.5.1 lumiHumanIDMapping_1.10.0 [11] annotate_1.34.1 gplots_2.11.0 [13] MASS_7.3-22 KernSmooth_2.23-8 [15] caTools_1.14 gdata_2.12.0 [17] gtools_2.7.0 limma_3.12.3 [19] lumiHumanAll.db_1.18.0 org.Hs.eg.db_2.7.1 [21] RSQLite_0.11.2 DBI_0.2-5 [23] AnnotationDbi_1.18.4 lumi_2.8.0 [25] nleqslv_2.0 methylumi_2.2.0 [27] ggplot2_0.9.3.1 reshape2_1.2.2 [29] scales_0.2.3 Biobase_2.16.0 [31] BiocGenerics_0.2.0

loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 bigmemory_4.4.3 [4] bigmemory.sri_0.1.2 biomaRt_2.12.0 Biostrings_2.24.1 [7] biovizBase_1.4.2 bitops_1.0-5 BSgenome_1.24.0 [10] cluster_1.14.3 colorspace_1.2-0 dichromat_2.0-0 [13] digest_0.5.2 GenomicFeatures_1.8.3 genoset_1.6.0 [16] gridExtra_0.9.1 gtable_0.1.2 hdrcde_2.16 [19] Hmisc_3.9-3 labeling_0.1 lattice_0.20-10 [22] Matrix_1.0-9 mgcv_1.7-22 munsell_0.4 [25] nlme_3.1-105 plyr_1.7.1 preprocessCore_1.18.0 [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-3 [31] Rsamtools_1.8.6 rtracklayer_1.16.3 snpStats_1.6.0 [34] splines_2.15.2 stats4_2.15.2 stringr_0.6.1 [37] survival_2.36-14 tools_2.15.2 VariantAnnotation_1.2.11 [40] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.2.0

On Thu, Apr 11, 2013 at 12:53 PM, Tengfei Yin notifications@github.comwrote:

Hi

Would you mind run sessionInfo()? this error is probably caused by package version difference.

Thanks

Tengfei

On Thu, Apr 11, 2013 at 10:53 AM, huwind notifications@github.com wrote:

First time to try autoplot after the installation. I followed the examples to get started, step by step.

autoplot(gr) Error in rep.int("", ncol(r)) : incorrect type for second argument

R version 2.15.2. Thanks for any tips!

— Reply to this email directly or view it on GitHub< https://github.com/tengfei/ggbio/issues/33> .

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274

— Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/33#issuecomment-16247158 .

— Reply to this email directly or view it on GitHub.

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274

modi2020 commented 10 years ago

Hi there,

I am stuck in the same problem. I did the updating step and reran the example but got the same error message again.

tengfei commented 10 years ago

Hi

Would you mind provide a minimal example and your sessionInfo()? that will help me identify the problem.

thanks

Tengfei

On Thu, Jan 2, 2014 at 1:29 PM, modi2020 notifications@github.com wrote:

Hi there,

I am stuck in the same problem. I did the updating step and reran the example but got the same error message again.

Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/33#issuecomment-31472895 .