I failed at the first step. The example dataset (skin) worked great, but I wasn't able to load the GTEx data (failed on Mac and Ubuntu).
Any ideas on how to proceed would be very much appreciated.
Thanks,
Jared
library(yarn)
obj <- downloadGTEx(type='genes',file='~/Desktop/gtex.rds')
Downloading and reading files
trying URL 'http://www.gtexportal.org/static/datasets/gtex_analysis_v6/annotations/GTEx_Data_V6_Annotations_SampleAttributesDS.txt'
Content type 'text/html' length 32619 bytes (31 KB)
==================================================
downloaded 31 KB
Parsed with column specification:
cols(
`<!DOCTYPE html>` = col_character()
)
Warning: 1 parsing failure.
row # A tibble: 1 x 5 col row col expected actual expected <int> <chr> <chr> <chr> actual 1 162 <NA> 1 columns 7 columns file # ... with 1 more variables: file <chr>
Error in pd[, "SAMPID"] : subscript out of bounds
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] yarn_1.2.0 Biobase_2.36.2 BiocGenerics_0.22.1 BiocInstaller_1.26.1
[5] dplyr_0.7.4 purrr_0.2.4 readr_1.1.1 tidyr_0.7.2
[9] tibble_1.3.4 ggplot2_2.2.1 tidyverse_1.1.1
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 siggenes_1.50.0 mclust_5.3
[4] XVector_0.16.0 GenomicRanges_1.28.6 quantro_1.10.0
[7] base64_2.0 bit64_0.9-7 AnnotationDbi_1.38.2
[10] lubridate_1.6.0 xml2_1.1.1 codetools_0.2-15
[13] splines_3.4.0 mnormt_1.5-5 doParallel_1.0.11
[16] jsonlite_1.5 Rsamtools_1.28.0 broom_0.4.2
[19] annotate_1.54.0 compiler_3.4.0 httr_1.3.1
[22] assertthat_0.2.0 Matrix_1.2-11 lazyeval_0.2.0
[25] limma_3.32.10 tools_3.4.0 bindrcpp_0.2
[28] gtable_0.2.0 glue_1.1.1 GenomeInfoDbData_0.99.0
[31] reshape2_1.4.2 doRNG_1.6.6 Rcpp_0.12.13
[34] cellranger_1.1.0 bumphunter_1.16.0 Biostrings_2.44.2
[37] multtest_2.32.0 gdata_2.18.0 preprocessCore_1.38.1
[40] nlme_3.1-131 rtracklayer_1.36.6 iterators_1.0.8
[43] psych_1.7.8 stringr_1.2.0 rvest_0.3.2
[46] rngtools_1.2.4 gtools_3.5.0 XML_3.98-1.9
[49] beanplot_1.2 edgeR_3.18.1 zlibbioc_1.22.0
[52] MASS_7.3-47 scales_0.5.0 hms_0.3
[55] SummarizedExperiment_1.6.5 GEOquery_2.42.0 minfi_1.22.1
[58] RColorBrewer_1.1-2 memoise_1.1.0 downloader_0.4
[61] pkgmaker_0.22 biomaRt_2.32.1 reshape_0.8.7
[64] stringi_1.1.5 RSQLite_2.0 genefilter_1.58.1
[67] S4Vectors_0.14.7 foreach_1.4.3 GenomicFeatures_1.28.5
[70] caTools_1.17.1 BiocParallel_1.10.1 GenomeInfoDb_1.12.3
[73] rlang_0.1.2 pkgconfig_2.0.1 matrixStats_0.52.2
[76] bitops_1.0-6 nor1mix_1.2-3 lattice_0.20-35
[79] bindr_0.1 GenomicAlignments_1.12.2 bit_1.1-12
[82] plyr_1.8.4 magrittr_1.5 R6_2.2.2
[85] IRanges_2.10.5 gplots_3.0.1 DelayedArray_0.2.7
[88] DBI_0.7 haven_1.1.0 foreign_0.8-69
[91] survival_2.41-3 RCurl_1.95-4.8 modelr_0.1.1
[94] KernSmooth_2.23-15 locfit_1.5-9.1 grid_3.4.0
[97] readxl_1.0.0 data.table_1.10.4-2 blob_1.1.0
[100] forcats_0.2.0 digest_0.6.12 xtable_1.8-2
[103] illuminaio_0.18.0 openssl_0.9.7 stats4_3.4.0
[106] munsell_0.4.3 registry_0.3 quadprog_1.5-5```
--
Ubuntu 14.04:
> library(yarn)
> obj <- downloadGTEx(type='genes',file='~/gtex.rds')
Downloading and reading files
downloaded 0 bytes
Error in download.file(url, method = method, ...) :
cannot download all files
In addition: Warning message:
In download.file(url, method = method, ...) :
URL 'https://www.gtexportal.org/static/datasets/gtex_analysis_v6/annotations/GTEx_Data_V6_Annotations_SampleAttributesDS.txt': status was 'Peer certificate cannot be authenticated with given CA certificates'
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] yarn_1.0.1 Biobase_2.34.0 BiocGenerics_0.20.0 dplyr_0.7.1 [5] purrr_0.2.2.2 readr_1.1.1 tidyr_0.6.3 tibble_1.3.3 [9] ggplot2_2.2.1 tidyverse_1.1.1 BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] colorspace_1.3-2 siggenes_1.48.0 mclust_5.3 [4] XVector_0.14.1 GenomicRanges_1.26.4 quantro_1.8.0 [7] base64_2.0 bit64_0.9-7 AnnotationDbi_1.36.2 [10] lubridate_1.6.0 xml2_1.1.1 codetools_0.2-15 [13] splines_3.3.3 mnormt_1.5-5 doParallel_1.0.11 [16] jsonlite_1.5 Rsamtools_1.26.2 broom_0.4.2 [19] annotate_1.52.1 httr_1.2.1 assertthat_0.2.0 [22] Matrix_1.2-10 lazyeval_0.2.0 limma_3.30.13 [25] tools_3.3.3 bindrcpp_0.2 gtable_0.2.0 [28] glue_1.1.1 reshape2_1.4.2 doRNG_1.6.6 [31] Rcpp_0.12.11 cellranger_1.1.0 bumphunter_1.14.0 [34] Biostrings_2.42.1 multtest_2.30.0 gdata_2.18.0 [37] preprocessCore_1.36.0 nlme_3.1-131 rtracklayer_1.34.2 [40] iterators_1.0.8 psych_1.7.5 stringr_1.2.0 [43] rvest_0.3.2 rngtools_1.2.4 gtools_3.5.0 [46] XML_3.98-1.9 beanplot_1.2 edgeR_3.16.5 [49] zlibbioc_1.20.0 MASS_7.3-47 scales_0.4.1 [52] hms_0.3 SummarizedExperiment_1.4.0 GEOquery_2.40.0 [55] minfi_1.20.2 RColorBrewer_1.1-2 memoise_1.1.0 [58] downloader_0.4 pkgmaker_0.22 biomaRt_2.30.0 [61] reshape_0.8.7 stringi_1.1.5 RSQLite_2.0 [64] genefilter_1.56.0 S4Vectors_0.12.2 foreach_1.4.3 [67] GenomicFeatures_1.26.4 caTools_1.17.1 BiocParallel_1.8.2 [70] GenomeInfoDb_1.10.3 rlang_0.1.1 pkgconfig_2.0.1 [73] matrixStats_0.52.2 bitops_1.0-6 nor1mix_1.2-3 [76] lattice_0.20-35 bindr_0.1 GenomicAlignments_1.10.1 [79] bit_1.1-12 plyr_1.8.4 magrittr_1.5 [82] R6_2.2.2 IRanges_2.8.2 gplots_3.0.1 [85] DBI_0.7 haven_1.0.0 foreign_0.8-69 [88] survival_2.41-3 RCurl_1.95-4.8 modelr_0.1.0 [91] KernSmooth_2.23-15 locfit_1.5-9.1 grid_3.3.3 [94] readxl_1.0.0 data.table_1.10.4 blob_1.1.0 [97] forcats_0.2.0 digest_0.6.12 xtable_1.8-2 [100] illuminaio_0.16.0 openssl_0.9.6 stats4_3.3.3 [103] munsell_0.4.3 registry_0.3 quadprog_1.5-5
--
I failed at the first step. The example dataset (skin) worked great, but I wasn't able to load the GTEx data (failed on Mac and Ubuntu).
Any ideas on how to proceed would be very much appreciated.
Thanks,
Jared