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svlachavas
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@svlachavas-7225
Last seen 13 months ago
Germany/Heidelberg/German Cancer Resear…
Dear All,
after installation through Bioconductor, I was trying to load a specific R package, named CVE, in order to perform variant prioritization: I tried to initially follow the vignette:
library(CVE)
Loading required package: tidyverse
-- Attaching packages --------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.2.1 v purrr 0.3.3
v tibble 2.1.3 v stringr 1.4.0
v tidyr 1.0.2 v forcats 0.4.0
v readr 1.3.1
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::arrange() masks plyr::arrange()
x purrr::compact() masks plyr::compact()
x dplyr::count() masks plyr::count()
x dplyr::failwith() masks plyr::failwith()
x dplyr::filter() masks stats::filter()
x dplyr::id() masks plyr::id()
x dplyr::lag() masks stats::lag()
x dplyr::mutate() masks plyr::mutate()
x dplyr::rename() masks plyr::rename()
x dplyr::summarise() masks plyr::summarise()
x dplyr::summarize() masks plyr::summarize()
library(RTCGAToolbox)
> crcData <- getFirehoseData(dataset="COAD",
+ clinical=TRUE,
+ Mutation=TRUE,
+ runDate="20160128")
Error: failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/"
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RTCGAToolbox_2.16.2 CVE_1.11.2 forcats_0.4.0
[4] stringr_1.4.0 purrr_0.3.3 readr_1.3.1
[7] tidyr_1.0.2 tibble_2.1.3 ggplot2_3.2.1
[10] tidyverse_1.3.0 dplyr_0.8.4 plyr_1.8.5
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 dynamicTreeCut_1.63-1
[3] htmlTable_1.13.3 XVector_0.26.0
[5] GenomicRanges_1.38.0 base64enc_0.1-3
[7] fs_1.3.1 rstudioapi_0.11
[9] bit64_0.9-7 AnnotationDbi_1.48.0
[11] fansi_0.4.1 mvtnorm_1.1-0
[13] lubridate_1.7.4 xml2_1.2.2
[15] codetools_0.2-16 splines_3.6.2
[17] doParallel_1.0.15 impute_1.60.0
[19] robustbase_0.93-5 knitr_1.28
[21] Formula_1.2-3 jsonlite_1.6.1
[23] broom_0.5.4 WGCNA_1.68
[25] cluster_2.1.0 GO.db_3.10.0
[27] dbplyr_1.4.2 png_0.1-7
[29] shiny_1.4.0 rrcov_1.5-2
[31] compiler_3.6.2 httr_1.4.1
[33] backports_1.1.5 fastmap_1.0.1
[35] assertthat_0.2.1 Matrix_1.2-18
[37] lazyeval_0.2.2 limma_3.42.2
[39] cli_2.0.1 later_1.0.0
[41] acepack_1.4.1 htmltools_0.4.0
[43] tools_3.6.2 GenomeInfoDbData_1.2.2
[45] gtable_0.3.0 glue_1.3.1
[47] Rcpp_1.0.3 Biobase_2.46.0
[49] cellranger_1.1.0 RJSONIO_1.3-1.4
[51] vctrs_0.2.3 RaggedExperiment_1.10.0
[53] gdata_2.18.0 ape_5.3
[55] preprocessCore_1.48.0 nlme_3.1-144
[57] iterators_1.0.12 xfun_0.12
[59] fastcluster_1.1.25 rvest_0.3.5
[61] mime_0.9 lifecycle_0.1.0
[63] gtools_3.8.1 XML_3.99-0.3
[65] DEoptimR_1.0-8 RCircos_1.2.1
[67] zlibbioc_1.32.0 MASS_7.3-51.5
[69] scales_1.1.0 promises_1.1.0
[71] hms_0.5.3 SummarizedExperiment_1.16.1
[73] parallel_3.6.2 RColorBrewer_1.1-2
[75] memoise_1.1.0 gridExtra_2.3
[77] rpart_4.1-15 latticeExtra_0.6-29
[79] stringi_1.4.6 RSQLite_2.2.0
[81] S4Vectors_0.24.3 pcaPP_1.9-73
[83] foreach_1.4.8 checkmate_2.0.0
[85] caTools_1.18.0 BiocGenerics_0.32.0
[87] BiocParallel_1.20.1 GenomeInfoDb_1.22.0
[89] rlang_0.4.4 pkgconfig_2.0.3
[91] matrixStats_0.55.0 bitops_1.0-6
[93] lattice_0.20-40 htmlwidgets_1.5.1
[95] bit_1.1-15.2 tidyselect_1.0.0
[97] robust_0.4-18.2 magrittr_1.5
[99] R6_2.4.1 IRanges_2.20.2
[101] gplots_3.0.3 generics_0.0.2
[103] Hmisc_4.3-1 fit.models_0.5-14
[105] DelayedArray_0.12.2 DBI_1.1.0
[107] pillar_1.4.3 haven_2.2.0
[109] foreign_0.8-75 withr_2.1.2
[111] RCurl_1.98-1.1 survival_3.1-8
[113] nnet_7.3-12 modelr_0.1.6
[115] crayon_1.3.4 KernSmooth_2.23-16
[117] jpeg_0.1-8.1 grid_3.6.2
[119] readxl_1.3.1 data.table_1.12.8
[121] blob_1.2.1 ConsensusClusterPlus_1.50.0
[123] reprex_0.3.0 digest_0.6.25
[125] xtable_1.8-4 httpuv_1.5.2
[127] stats4_3.6.2 munsell_0.5.0
As you can see from the above error, I could not load any data, which was also the case when I tried other similar functions. Is there a possibility for the error due to plyr-dplyr conflicts from tidyverse ? Or something different with my internet connection and/or settings ? I also run Rstudio as administrator.
Thank you in advance,
Efstathios
What happens if you restart R (and make sure you aren't loading any
.RDatafiles back into your workspace) and just try fetching dat without loading the CVA package, ie. from a clean R sesion, just do:Do you still get the same error?
Dear Steve, thank you for your suggestion and excuse me for the late reply. Unfortunately, the error continues to appear even if do not load the CVE package:
Error: failed to load external entity "http://gdac.broadinstitute.org/runs/stddata_201601_28/data/COAD/20160128/"
Well, it appears to be some type of connectivity problem on your end. I just tried this on my machine (macOS), and it worked without any problems.
I'm not familiar with how to best configure things like
option(download.file.method)and other things to get internet downloads to work well on windows, but I feel like I often see internet connectivity issues tied to R running on windows ... and Martin usually swings in to help debug people's way to a fix.There are also many posts about dealing with weird proxy issues that might be tripping you up to.
Try to dig through the support board using google to search, and append
site:support.bioconductor.ogto the end of the query so you can search this site a bit better than the search bar here.Dear Steve, thank you for your consideration on this matter !! This is really strange, as it is the first time I have encountered this-perhaps the tidyverse R package and the mentioned conflicts are irrelevant-I thought removing tidyverse with tidyr and dplyr and re-install again, but I'm not certain it is the point...Nevertheless i will take a look into your suggestions and search other posts