Error in GDCprepare step of TCGAbiolinks

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Error in GDCprepare step of TCGAbiolinks

Ankita Lawarde
   Dear Sir/ma'am,

I'm using R-3.4.4 and TCGAbiolinks package for the analysis of GDC data.
Till today i have reintalled R and R studio for 5 times but one error comes
when i analyze the GDC data at the step GDCprepare. the data i am using is
not a legacy data of GDC data portal.

I think the problem is with my Laptop only because i have run the same
commands in another PC and there was no error. Thus i have uninstalled and
again installed the R but the error is not going.

Today i have installed the developer version of TCGAbiolinks. and the error
is still there.

I have attached the code used and the session info.

Every time i run this GDCprepare command this same error comes as biomart
service is not available. So i had contaced the Biomart people but they
said that the Biomart is working fine.

below is the complete R code i am usign with the corresponding error,

library(TCGAbiolinks)

query.exp <- GDCquery(project = "TCGA-LUAD",
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "HTSeq - Counts",
                      experimental.strategy = "RNA-Seq")

query_load <- GDCdownload(query.exp)

luad.exp <- GDCprepare(query = query.exp, save = TRUE, save.filename =
"TCGA_LUAD_Exp.rda",
                       summarizedExperiment = TRUE)

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Starting to add information to samples
 => Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=>
http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
 => Adding subtype information to samples
luad subtype information from:doi:10.1038/nature13385
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
Error: $ operator is invalid for atomic vectors


 sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] TCGAbiolinks_2.7.21        SummarizedExperiment_1.8.1
DelayedArray_0.4.1         matrixStats_0.53.1
 [5] Biobase_2.38.0             GenomicRanges_1.30.0
 GenomeInfoDb_1.14.0        IRanges_2.12.0
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0
RColorBrewer_1.1-2         edgeR_3.20.9
[13] limma_3.34.9

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            selectr_0.3-2               rjson_0.2.15

  [4] hwriter_1.3.2               circlize_0.4.3
XVector_0.18.0
  [7] GlobalOptions_0.0.13        ggpubr_0.1.6                matlab_1.0.2

 [10] ggrepel_0.7.0               bit64_0.9-7
 AnnotationDbi_1.40.0
 [13] xml2_1.2.0                  codetools_0.2-15
splines_3.4.4
 [16] R.methodsS3_1.7.1           mnormt_1.5-5
doParallel_1.0.11
 [19] DESeq_1.30.0                geneplotter_1.56.0          knitr_1.20

 [22] jsonlite_1.5                Rsamtools_1.30.0            km.ci_0.5-2

 [25] broom_0.4.3                 annotate_1.56.1
 cluster_2.0.6
 [28] R.oo_1.21.0                 readr_1.1.1
 compiler_3.4.4
 [31] httr_1.3.1                  assertthat_0.2.0
Matrix_1.2-12
 [34] lazyeval_0.2.1              prettyunits_1.0.2           tools_3.4.4

 [37] bindrcpp_0.2                gtable_0.2.0                glue_1.2.0

 [40] GenomeInfoDbData_1.0.0      reshape2_1.4.3              dplyr_0.7.4

 [43] ggthemes_3.4.0              ShortRead_1.36.1            Rcpp_0.12.16

 [46] Biostrings_2.46.0           nlme_3.1-131.1
rtracklayer_1.38.3
 [49] iterators_1.0.9             psych_1.7.8
 stringr_1.3.0
 [52] rvest_0.3.2                 XML_3.98-1.10               zoo_1.8-1

 [55] zlibbioc_1.24.0             scales_0.5.0
aroma.light_3.8.0
 [58] hms_0.4.2                   curl_3.1
ComplexHeatmap_1.17.1
 [61] memoise_1.1.0               gridExtra_2.3               KMsurv_0.1-5

 [64] ggplot2_2.2.1               downloader_0.4
biomaRt_2.34.2
 [67] latticeExtra_0.6-28         stringi_1.1.7               RSQLite_2.0

 [70] genefilter_1.60.0           foreach_1.4.4
 RMySQL_0.10.14
 [73] GenomicFeatures_1.30.3      BiocParallel_1.12.0         shape_1.4.4

 [76] rlang_0.2.0                 pkgconfig_2.0.1             bitops_1.0-6

 [79] lattice_0.20-35             purrr_0.2.4                 bindr_0.1.1

 [82] GenomicAlignments_1.14.1    cmprsk_2.2-7                bit_1.1-12

 [85] plyr_1.8.4                  magrittr_1.5                R6_2.2.2

 [88] DBI_0.8                     mgcv_1.8-23                 pillar_1.2.1

 [91] foreign_0.8-69              survival_2.41-3
 RCurl_1.95-4.10
 [94] tibble_1.4.2                EDASeq_2.12.0
 survMisc_0.5.4
 [97] GetoptLong_0.1.6            progress_1.1.2
locfit_1.5-9.1
[100] grid_3.4.4                  sva_3.26.0
data.table_1.10.4-3
[103] blob_1.1.0                  ConsensusClusterPlus_1.42.0
digest_0.6.15
[106] xtable_1.8-2                tidyr_0.8.0
 R.utils_2.6.0
[109] munsell_0.4.3               survminer_0.4.2




I hope this helps to understand my problem.
 I look forward to hear from you



Regards,
Ankita

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