Error in GDCquery

[joseluischinito]

Hi

When I run following things in R it makes error.

query.exp <- GDCquery(project = "TCGA-KIRC", legacy = TRUE, data.category = "Gene expression", data.type = "Gene expression quantification", platform = "Illumina HiSeq", file.type = "results", experimental.strategy = "RNA-Seq", sample.type = c("Primary solid Tumor","Solid Tissue Normal"))

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-KIRC
Error:  Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:
  URL: https://gdc-api.nci.nih.gov/legacy/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=7757&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-KIRC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Gene%20expression%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20expression%20quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.platform%22,%22value%22:[%22Illumina%20HiSeq%22]%7D%7D]%7D&format=JSON
  error: Failure when receiving data from the peer

We will retry to access GDC!
Error in if (json$data$pagination$count == 0) { : 
  argument is of length zero

Yesterday it executed well

[driesvr]

I have the same issue. Accessing the URL directly still works though - for this example the pagecount is 1771.

[SiddeshRao]

Having the same issue. Seems like there is some issue accessing the URL through GDCquery

[ZhangQiuxue]

I have the same issue.

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-STAD
Error:  Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:
  URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2203&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-STAD%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22miRNA%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22BCGSC%20miRNA%20Profiling%22]%7D%7D]%7D&format=JSON
  error: SSLRead() return error -9806

[superwang2018]

Having the same issue, too.

[tiagochst]

It seems it is a curl problem. Could. you send me the sessionInfo()? Also, could you verify you have the last version available ? https://github.com/jeroen/curl

This type of errors seems not to be new: https://stackoverflow.com/questions/39116617/os-x-10-11-6-el-capitan-sslread-return-error-9841

[joseluischinito]

Ok, sessionInfo()

`R version 3.4.4 (2018-03-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252
[3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Mexico.1252

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

loaded via a namespace (and not attached): [1] tidyselect_0.2.4 purrr_0.2.4 reshape2_1.4.3 kernlab_0.9-26
[5] splines_3.4.4 lattice_0.20-35 colorspace_1.3-2 stats4_3.4.4
[9] geometry_0.3-6 survival_2.41-3 prodlim_2018.04.18 rlang_0.2.0
[13] ModelMetrics_1.1.0 pillar_1.2.3 withr_2.1.2 foreign_0.8-69
[17] glue_1.2.0 bindrcpp_0.2.2 foreach_1.4.4 bindr_0.1.1
[21] plyr_1.8.4 dimRed_0.1.0 lava_1.6.1 robustbase_0.93-0 [25] stringr_1.3.1 timeDate_3043.102 munsell_0.4.3 gtable_0.2.0
[29] recipes_0.1.2 codetools_0.2-15 psych_1.8.4 magic_1.5-8
[33] caret_6.0-79 parallel_3.4.4 class_7.3-14 DEoptimR_1.0-8
[37] broom_0.4.4 Rcpp_0.12.17 scales_0.5.0 ipred_0.9-6
[41] CVST_0.2-1 abind_1.4-5 mnormt_1.5-5 ggplot2_2.2.1
[45] stringi_1.1.7 dplyr_0.7.5 RcppRoll_0.2.2 ddalpha_1.3.3
[49] grid_3.4.4 tools_3.4.4 magrittr_1.5 lazyeval_0.2.1
[53] tibble_1.4.2 tidyr_0.8.1 DRR_0.0.3 pkgconfig_2.0.1
[57] MASS_7.3-49 Matrix_1.2-12 lubridate_1.7.4 gower_0.1.2
[61] assertthat_0.2.0 iterators_1.0.9 R6_2.2.2 rpart_4.1-13
[65] sfsmisc_1.1-2 nnet_7.3-12 nlme_3.1-131.1 compiler_3.4.4`

curl version

curl 7.55.1 (Windows) libcurl/7.55.1 WinSSL
Release-Date: [unreleased]
Protocols: dict file ftp ftps http https imap imaps pop3 pop3s smtp smtps telnet tftp
Features: AsynchDNS IPv6 Largefile SSPI Kerberos SPNEGO NTLM SSL

But my error is "Failure when receiving data from the peer" and not "sslread()"

[SiddeshRao]

sessionInfo() R version 3.4.3 (2017-11-30) 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] stats4 parallel stats graphics grDevices utils datasets methods
[9] base

other attached packages: [1] gaia_2.22.0 GenomicFeatures_1.30.3 AnnotationDbi_1.40.0
[4] Biobase_2.38.0 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0
[7] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0
[10] GenomicDataCommons_1.5.3 magrittr_1.5 TCGAbiolinks_2.6.12
[13] httr_1.3.1 stringi_1.1.7 curl_3.2

loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.4-1 rjson_0.2.19
[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_0.8.0 bit64_0.9-7 xml2_1.2.0
[13] codetools_0.2-15 splines_3.4.3 R.methodsS3_1.7.1
[16] mnormt_1.5-5 doParallel_1.0.11 DESeq_1.30.0
[19] geneplotter_1.56.0 knitr_1.20 jsonlite_1.5
[22] Rsamtools_1.30.0 km.ci_0.5-2 broom_0.4.4
[25] annotate_1.56.2 cluster_2.0.7-1 R.oo_1.22.0
[28] readr_1.1.1 compiler_3.4.3 assertthat_0.2.0
[31] Matrix_1.2-14 lazyeval_0.2.1 limma_3.34.9
[34] prettyunits_1.0.2 tools_3.4.3 bindrcpp_0.2.2
[37] gtable_0.2.0 glue_1.2.0 GenomeInfoDbData_1.0.0
[40] reshape2_1.4.3 dplyr_0.7.5 rappdirs_0.3.1
[43] ggthemes_3.5.0 ShortRead_1.36.1 Rcpp_0.12.17
[46] Biostrings_2.46.0 nlme_3.1-137 rtracklayer_1.38.3
[49] iterators_1.0.9 psych_1.8.4 stringr_1.3.1
[52] rvest_0.3.2 XML_3.98-1.11 edgeR_3.20.9
[55] zoo_1.8-1 zlibbioc_1.24.0 scales_0.5.0
[58] aroma.light_3.8.0 hms_0.4.2 SummarizedExperiment_1.8.1 [61] RColorBrewer_1.1-2 ComplexHeatmap_1.17.1 memoise_1.1.0
[64] gridExtra_2.3 KMsurv_0.1-5 ggplot2_2.2.1
[67] downloader_0.4 biomaRt_2.34.2 latticeExtra_0.6-28
[70] RSQLite_2.1.1 genefilter_1.60.0 foreach_1.4.4
[73] RMySQL_0.10.15 BiocParallel_1.12.0 shape_1.4.4
[76] rlang_0.2.0 pkgconfig_2.0.1 matrixStats_0.53.1
[79] bitops_1.0-6 lattice_0.20-35 purrr_0.2.4
[82] bindr_0.1.1 cmprsk_2.2-7 GenomicAlignments_1.14.2
[85] bit_1.1-13 tidyselect_0.2.4 plyr_1.8.4
[88] R6_2.2.2 DelayedArray_0.4.1 DBI_1.0.0
[91] mgcv_1.8-23 pillar_1.2.3 foreign_0.8-70
[94] survival_2.42-3 RCurl_1.95-4.10 tibble_1.4.2
[97] EDASeq_2.12.0 survMisc_0.5.4 GetoptLong_0.1.6
[100] progress_1.1.2 locfit_1.5-9.1 grid_3.4.3
[103] sva_3.26.0 data.table_1.11.2 blob_1.1.1
[106] ConsensusClusterPlus_1.42.0 digest_0.6.15 xtable_1.8-2
[109] tidyr_0.8.1 R.utils_2.6.0 munsell_0.4.3
[112] survminer_0.4.2

[superwang2018]

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] TCGAbiolinks_2.8.0

loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.4-1 rjson_0.2.19
[4] hwriter_1.3.2 circlize_0.4.3 XVector_0.20.0
[7] GenomicRanges_1.32.3 GlobalOptions_0.0.13 ggpubr_0.1.6
[10] matlab_1.0.2 ggrepel_0.8.0 bit64_0.9-7
[13] AnnotationDbi_1.42.1 xml2_1.2.0 codetools_0.2-15
[16] splines_3.5.0 R.methodsS3_1.7.1 mnormt_1.5-5
[19] doParallel_1.0.11 DESeq_1.32.0 geneplotter_1.58.0
[22] knitr_1.20 jsonlite_1.5 Rsamtools_1.32.0
[25] km.ci_0.5-2 broom_0.4.4 annotate_1.58.0
[28] cluster_2.0.7-1 R.oo_1.22.0 readr_1.1.1
[31] compiler_3.5.0 httr_1.3.1 assertthat_0.2.0
[34] Matrix_1.2-14 lazyeval_0.2.1 limma_3.36.1
[37] prettyunits_1.0.2 tools_3.5.0 bindrcpp_0.2.2
[40] gtable_0.2.0 glue_1.2.0 GenomeInfoDbData_1.1.0
[43] reshape2_1.4.3 dplyr_0.7.5 ggthemes_3.5.0
[46] ShortRead_1.38.0 Rcpp_0.12.17 Biobase_2.40.0
[49] Biostrings_2.48.0 nlme_3.1-137 rtracklayer_1.40.2
[52] iterators_1.0.9 psych_1.8.4 stringr_1.3.1
[55] rvest_0.3.2 XML_3.98-1.11 edgeR_3.22.2
[58] zoo_1.8-1 zlibbioc_1.26.0 scales_0.5.0
[61] aroma.light_3.10.0 hms_0.4.2 parallel_3.5.0
[64] SummarizedExperiment_1.10.1 RColorBrewer_1.1-2 ComplexHeatmap_1.18.0
[67] yaml_2.1.19 memoise_1.1.0 gridExtra_2.3
[70] KMsurv_0.1-5 ggplot2_2.2.1 downloader_0.4
[73] biomaRt_2.36.1 latticeExtra_0.6-28 stringi_1.1.7
[76] RSQLite_2.1.1 genefilter_1.62.0 S4Vectors_0.18.2
[79] foreach_1.4.4 GenomicFeatures_1.32.0 BiocGenerics_0.26.0
[82] BiocParallel_1.14.1 shape_1.4.4 GenomeInfoDb_1.16.0
[85] rlang_0.2.0 pkgconfig_2.0.1 matrixStats_0.53.1
[88] bitops_1.0-6 lattice_0.20-35 purrr_0.2.4
[91] bindr_0.1.1 GenomicAlignments_1.16.0 cmprsk_2.2-7
[94] bit_1.1-13 tidyselect_0.2.4 plyr_1.8.4
[97] magrittr_1.5 R6_2.2.2 IRanges_2.14.10
[100] DelayedArray_0.6.0 DBI_1.0.0 mgcv_1.8-23
[103] pillar_1.2.3 foreign_0.8-70 survival_2.41-3
[106] RCurl_1.95-4.10 tibble_1.4.2 EDASeq_2.14.0
[109] survMisc_0.5.4 GetoptLong_0.1.6 progress_1.1.2
[112] locfit_1.5-9.1 grid_3.5.0 sva_3.28.0
[115] data.table_1.11.2 blob_1.1.1 ConsensusClusterPlus_1.44.0 [118] digest_0.6.15 xtable_1.8-2 tidyr_0.8.1
[121] R.utils_2.6.0 stats4_3.5.0 munsell_0.4.3
[124] survminer_0.4.2

[dannyteng1971]

dear alls I am suffered from same problem since 2 days ago. ""Error in getURL(url, GET, timeout(600)) : 'getURL()' failed:" the following code can not work if sample is ""TCGA-COAD""( ps: other is ok)

query.exp2222 <- GDCquery(project = "TCGA-COAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ") this failue query.exp2222 <- GDCquery(project = "TCGA-READ", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ") this ok

error message Error in getURL(url, GET, timeout(600)) : 'getURL()' failed: URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2493&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-COAD%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20FPKM-UQ%22]%7D%7D]%7D&format=JSON error: Failure when receiving data from the peer In addition: Warning message: In date_names_lang(date_names) : restarting interrupted promise evaluation

thanks

[atakanekiz]

I have the same problem:

Error in is.response(x) : 'getURL()' failed:
  URL: https://gdc-api.nci.nih.gov/cases/?pretty=true&expand=diagnoses,diagnoses.treatments,annotations,family_histories,demographic,exposures&size=470&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-SKCM%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Clinical%22]%7D%7D]%7D&format=json
  error: Failure when receiving data from the peer

Session details:

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
[1] TCGAbiolinks_2.8.0

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            selectr_0.4-1               rjson_0.2.19                hwriter_1.3.2              
  [5] circlize_0.4.3              XVector_0.20.0              GenomicRanges_1.32.3        GlobalOptions_0.0.13       
  [9] ggpubr_0.1.6                matlab_1.0.2                ggrepel_0.8.0               bit64_0.9-7                
 [13] AnnotationDbi_1.42.1        xml2_1.2.0                  codetools_0.2-15            splines_3.5.0              
 [17] R.methodsS3_1.7.1           mnormt_1.5-5                doParallel_1.0.11           DESeq_1.32.0               
 [21] geneplotter_1.58.0          knitr_1.20                  jsonlite_1.5                Rsamtools_1.32.0           
 [25] km.ci_0.5-2                 broom_0.4.4                 annotate_1.58.0             cluster_2.0.7-1            
 [29] R.oo_1.22.0                 readr_1.1.1                 compiler_3.5.0              httr_1.3.1                 
 [33] assertthat_0.2.0            Matrix_1.2-14               lazyeval_0.2.1              limma_3.36.1               
 [37] prettyunits_1.0.2           tools_3.5.0                 bindrcpp_0.2.2              gtable_0.2.0               
 [41] glue_1.2.0                  GenomeInfoDbData_1.1.0      reshape2_1.4.3              dplyr_0.7.5                
 [45] ggthemes_3.5.0              ShortRead_1.38.0            Rcpp_0.12.17                Biobase_2.40.0             
 [49] Biostrings_2.48.0           nlme_3.1-137                rtracklayer_1.40.2          iterators_1.0.9            
 [53] psych_1.8.4                 stringr_1.3.1               rvest_0.3.2                 XML_3.98-1.11              
 [57] edgeR_3.22.2                zoo_1.8-1                   zlibbioc_1.26.0             scales_0.5.0               
 [61] aroma.light_3.10.0          hms_0.4.2                   parallel_3.5.0              SummarizedExperiment_1.10.1
 [65] RColorBrewer_1.1-2          curl_3.2                    ComplexHeatmap_1.18.0       yaml_2.1.19                
 [69] memoise_1.1.0               gridExtra_2.3               KMsurv_0.1-5                ggplot2_2.2.1              
 [73] downloader_0.4              biomaRt_2.36.1              latticeExtra_0.6-28         stringi_1.1.7              
 [77] RSQLite_2.1.1               genefilter_1.62.0           S4Vectors_0.18.2            foreach_1.4.4              
 [81] GenomicFeatures_1.32.0      BiocGenerics_0.26.0         BiocParallel_1.14.1         shape_1.4.4                
 [85] GenomeInfoDb_1.16.0         rlang_0.2.0                 pkgconfig_2.0.1             matrixStats_0.53.1         
 [89] bitops_1.0-6                lattice_0.20-35             purrr_0.2.4                 bindr_0.1.1                
 [93] GenomicAlignments_1.16.0    cmprsk_2.2-7                bit_1.1-13                  tidyselect_0.2.4           
 [97] plyr_1.8.4                  magrittr_1.5                R6_2.2.2                    IRanges_2.14.10            
[101] DelayedArray_0.6.0          DBI_1.0.0                   mgcv_1.8-23                 pillar_1.2.3               
[105] foreign_0.8-70              survival_2.41-3             RCurl_1.95-4.10             tibble_1.4.2               
[109] EDASeq_2.14.0               survMisc_0.5.4              GetoptLong_0.1.6            progress_1.1.2             
[113] locfit_1.5-9.1              grid_3.5.0                  sva_3.28.0                  data.table_1.11.4          
[117] blob_1.1.1                  ConsensusClusterPlus_1.44.0 digest_0.6.15               xtable_1.8-2               
[121] tidyr_0.8.1                 R.utils_2.6.0               stats4_3.5.0                munsell_0.4.3              
[125] survminer_0.4.2  

I updated my curl to the latest version:

(In command prompt)

C:\Users\ataka>curl --version
curl 7.60.0 (x86_64-pc-win32) libcurl/7.60.0 OpenSSL/1.1.0h (WinSSL) zlib/1.2.11 brotli/1.0.4 WinIDN libssh2/1.8.0 nghttp2/1.32.0
Release-Date: 2018-05-16
Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtsp scp sftp smb smbs smtp smtps telnet tftp
Features: AsynchDNS IDN IPv6 Largefile SSPI Kerberos SPNEGO NTLM SSL libz brotli TLS-SRP HTTP2 HTTPS-proxy MultiSSL

Also updated curl in RStudio

> curl_version()
$`version`
[1] "7.59.0"

$ssl_version
[1] "(OpenSSL/1.0.2n) WinSSL"

$libz_version
[1] "1.2.8"

$libssh_version
[1] "libssh2/1.8.0"

$libidn_version
[1] NA

$host
[1] "x86_64-w64-mingw32"

$protocols
 [1] "dict"   "file"   "ftp"    "ftps"   "gopher" "http"   "https"  "imap"   "imaps"  "ldap"   "ldaps" 
[12] "pop3"   "pop3s"  "rtsp"   "scp"    "sftp"   "smtp"   "smtps"  "telnet" "tftp"  

$ipv6
[1] TRUE

$http2
[1] FALSE

$idn
[1] TRUE

[dannyteng1971]

​yes, i update the curl package but it still not work. it is a ? bug that

TCGA-READ is ok but TCGA-COAD fail? it seem be associted with project-specific did you have any comment???

query.expTTT <- GDCquery(project = "TCGA-COAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ")

the following is my sessioninfo()

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Traditional)_Taiwan.950 LC_CTYPE=Chinese (Traditional)_Taiwan.950 [3] LC_MONETARY=Chinese (Traditional)_Taiwan.950 LC_NUMERIC=C

[5] LC_TIME=Chinese (Traditional)_Taiwan.950

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

other attached packages: [1] curl_3.2 TCGAbiolinks_2.9.0 stringi_1.1.7

loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.4-1 rjson_0.2.19 hwriter_1.3.2 [5] circlize_0.4.3 XVector_0.20.0 GenomicRanges_1.32.3 GlobalOptions_0.0.13 [9] ggpubr_0.1.6 matlab_1.0.2 ggrepel_0.8.0 bit64_0.9-7 [13] AnnotationDbi_1.42.1 xml2_1.2.0 codetools_0.2-15 splines_3.5.0 [17] R.methodsS3_1.7.1 mnormt_1.5-5 doParallel_1.0.11 DESeq_1.32.0 [21] geneplotter_1.58.0 knitr_1.20 jsonlite_1.5 Rsamtools_1.32.0 [25] km.ci_0.5-2 broom_0.4.4 annotate_1.58.0 cluster_2.0.7-1 [29] R.oo_1.22.0 readr_1.1.1 compiler_3.5.0 httr_1.3.1 [33] assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1 limma_3.36.1 [37] prettyunits_1.0.2 tools_3.5.0 bindrcpp_0.2.2 gtable_0.2.0 [41] glue_1.2.0 GenomeInfoDbData_1.1.0 reshape2_1.4.3 dplyr_0.7.5 [45] ggthemes_3.5.0 ShortRead_1.38.0 Rcpp_0.12.17 Biobase_2.40.0 [49] Biostrings_2.48.0 nlme_3.1-137 rtracklayer_1.40.2 iterators_1.0.9 [53] psych_1.8.4 stringr_1.3.1 rvest_0.3.2 XML_3.98-1.11 [57] edgeR_3.22.2 zoo_1.8-1 zlibbioc_1.26.0 scales_0.5.0 [61] aroma.light_3.10.0 hms_0.4.2 parallel_3.5.0 SummarizedExperiment_1.10.1 [65] RColorBrewer_1.1-2 ComplexHeatmap_1.18.0 memoise_1.1.0 gridExtra_2.3 [69] KMsurv_0.1-5 ggplot2_2.2.1 downloader_0.4 biomaRt_2.36.1 [73] latticeExtra_0.6-28 RSQLite_2.1.1 genefilter_1.62.0 S4Vectors_0.18.2 [77] foreach_1.4.4 GenomicFeatures_1.32.0 BiocGenerics_0.26.0 BiocParallel_1.14.1 [81] shape_1.4.4 GenomeInfoDb_1.16.0 rlang_0.2.1 pkgconfig_2.0.1 [85] matrixStats_0.53.1 bitops_1.0-6 lattice_0.20-35 purrr_0.2.5 [89] bindr_0.1.1 cmprsk_2.2-7 GenomicAlignments_1.16.0 bit_1.1-14 [93] tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5 R6_2.2.2 [97] IRanges_2.14.10 DelayedArray_0.6.0 DBI_1.0.0 mgcv_1.8-23 [101] pillar_1.2.3 foreign_0.8-70 survival_2.41-3 RCurl_1.95-4.10 [105] tibble_1.4.2 EDASeq_2.14.0 survMisc_0.5.4 GetoptLong_0.1.6 [109] progress_1.1.2 locfit_1.5-9.1 grid_3.5.0 sva_3.28.0 [113] data.table_1.11.4 blob_1.1.1 ConsensusClusterPlus_1.44.0 digest_0.6.15 [117] xtable_1.8-2 tidyr_0.8.1 R.utils_2.6.0 stats4_3.5.0 [121] munsell_0.4.3 survminer_0.4.2

thanks ​ [image: Mailtrack] https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& Sender notified by Mailtrack https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& 06/03/18, 11:08:35 PM

2018-06-03 7:26 GMT+08:00 atakanekiz notifications@github.com:

I have the same problem:

Error in is.response(x) : 'getURL()' failed: URL: https://gdc-api.nci.nih.gov/cases/?pretty=true&expand=diagnoses,diagnoses.treatments,annotations,family_histories,demographic,exposures&size=470&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-SKCM%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Clinical%22]%7D%7D]%7D&format=json error: Failure when receiving data from the peer

Session details:

R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] TCGAbiolinks_2.8.0

loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.4-1 rjson_0.2.19 hwriter_1.3.2 [5] circlize_0.4.3 XVector_0.20.0 GenomicRanges_1.32.3 GlobalOptions_0.0.13 [9] ggpubr_0.1.6 matlab_1.0.2 ggrepel_0.8.0 bit64_0.9-7 [13] AnnotationDbi_1.42.1 xml2_1.2.0 codetools_0.2-15 splines_3.5.0 [17] R.methodsS3_1.7.1 mnormt_1.5-5 doParallel_1.0.11 DESeq_1.32.0 [21] geneplotter_1.58.0 knitr_1.20 jsonlite_1.5 Rsamtools_1.32.0 [25] km.ci_0.5-2 broom_0.4.4 annotate_1.58.0 cluster_2.0.7-1 [29] R.oo_1.22.0 readr_1.1.1 compiler_3.5.0 httr_1.3.1 [33] assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1 limma_3.36.1 [37] prettyunits_1.0.2 tools_3.5.0 bindrcpp_0.2.2 gtable_0.2.0 [41] glue_1.2.0 GenomeInfoDbData_1.1.0 reshape2_1.4.3 dplyr_0.7.5 [45] ggthemes_3.5.0 ShortRead_1.38.0 Rcpp_0.12.17 Biobase_2.40.0 [49] Biostrings_2.48.0 nlme_3.1-137 rtracklayer_1.40.2 iterators_1.0.9 [53] psych_1.8.4 stringr_1.3.1 rvest_0.3.2 XML_3.98-1.11 [57] edgeR_3.22.2 zoo_1.8-1 zlibbioc_1.26.0 scales_0.5.0 [61] aroma.light_3.10.0 hms_0.4.2 parallel_3.5.0 SummarizedExperiment_1.10.1 [65] RColorBrewer_1.1-2 curl_3.2 ComplexHeatmap_1.18.0 yaml_2.1.19 [69] memoise_1.1.0 gridExtra_2.3 KMsurv_0.1-5 ggplot2_2.2.1 [73] downloader_0.4 biomaRt_2.36.1 latticeExtra_0.6-28 stringi_1.1.7 [77] RSQLite_2.1.1 genefilter_1.62.0 S4Vectors_0.18.2 foreach_1.4.4 [81] GenomicFeatures_1.32.0 BiocGenerics_0.26.0 BiocParallel_1.14.1 shape_1.4.4 [85] GenomeInfoDb_1.16.0 rlang_0.2.0 pkgconfig_2.0.1 matrixStats_0.53.1 [89] bitops_1.0-6 lattice_0.20-35 purrr_0.2.4 bindr_0.1.1 [93] GenomicAlignments_1.16.0 cmprsk_2.2-7 bit_1.1-13 tidyselect_0.2.4 [97] plyr_1.8.4 magrittr_1.5 R6_2.2.2 IRanges_2.14.10 [101] DelayedArray_0.6.0 DBI_1.0.0 mgcv_1.8-23 pillar_1.2.3 [105] foreign_0.8-70 survival_2.41-3 RCurl_1.95-4.10 tibble_1.4.2 [109] EDASeq_2.14.0 survMisc_0.5.4 GetoptLong_0.1.6 progress_1.1.2 [113] locfit_1.5-9.1 grid_3.5.0 sva_3.28.0 data.table_1.11.4 [117] blob_1.1.1 ConsensusClusterPlus_1.44.0 digest_0.6.15 xtable_1.8-2 [121] tidyr_0.8.1 R.utils_2.6.0 stats4_3.5.0 munsell_0.4.3 [125] survminer_0.4.2

I updated my curl to the latest version:

(In command prompt)

C:\Users\ataka>curl --version curl 7.60.0 (x86_64-pc-win32) libcurl/7.60.0 OpenSSL/1.1.0h (WinSSL) zlib/1.2.11 brotli/1.0.4 WinIDN libssh2/1.8.0 nghttp2/1.32.0 Release-Date: 2018-05-16 Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtsp scp sftp smb smbs smtp smtps telnet tftp Features: AsynchDNS IDN IPv6 Largefile SSPI Kerberos SPNEGO NTLM SSL libz brotli TLS-SRP HTTP2 HTTPS-proxy MultiSSL

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/216#issuecomment-394123934, or mute the thread https://github.com/notifications/unsubscribe-auth/Al9STHs_rc7iVkB-UpsCw2aiaJtNUpRGks5t4x8mgaJpZM4UOu5H .

-- Hao-Wei Teng MD and Ph.D. 血液學和腫瘤學 鄧豪偉，台北榮總 腫瘤內科 陽明大學 兼任副教授 http://crc.uptocare.com/ http://uptocare.com/

[dannyteng1971]

I THINK curl_version() $version [1] "7.59.0" AND PROBLEM IS NOT AT HERE, because, some projects work, such as ""TCGA-READ"" but ""TCGA-COAD"" fail is anyone have commet

[atakanekiz]

TCGA-READ didn't work for me, although the URL opens up in the browser when I try it. That seems to suggest that there is something wrong in the curl protocol within R Studio.

[tiagochst]

I updated the package some curl versions were not able to redirect the new api. It should be fixed now. Could you, please, update the package from GitHub with:

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")

[ghost]

This fix worked for me.

[atakanekiz]

Works for me as well. Thanks!

[superwang2018]

The issue was settled! Thank you!

[joseluischinito]

Thanks!! worked for me too

[mbk0asis]

Help! I got a following error after install the updates.

Error: package or namespace load failed for ‘TCGAbiolinks’ in get(Info[i, 1], envir = env):
 lazy-load database '/home/bio0/R/x86_64-pc-linux-gnu-library/3.4/data.table/R/data.table.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

session info

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        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               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] DT_0.4

loaded via a namespace (and not attached):
  [1] circlize_0.4.3              aroma.light_3.8.0           plyr_1.8.4                  selectr_0.4-1               ConsensusClusterPlus_1.42.0 lazyeval_0.2.1             
  [7] splines_3.4.4               BiocParallel_1.12.0         GenomeInfoDb_1.14.0         ggplot2_2.2.1               sva_3.26.0                  digest_0.6.15              
 [13] foreach_1.4.4               BiocInstaller_1.28.0        htmltools_0.3.6             magrittr_1.5                memoise_1.1.0               cluster_2.0.7-1            
 [19] doParallel_1.0.11           limma_3.34.9                ComplexHeatmap_1.17.1       Biostrings_2.46.0           readr_1.1.1                 annotate_1.56.2            
 [25] matrixStats_0.53.1          R.utils_2.6.0               prettyunits_1.0.2           colorspace_1.3-2            blob_1.1.1                  rvest_0.3.2                
 [31] ggrepel_0.8.0               RCurl_1.95-4.10             jsonlite_1.5                genefilter_1.60.0           bindr_0.1.1                 survival_2.42-3            
 [37] zoo_1.8-1                   iterators_1.0.9             glue_1.2.0                  survminer_0.4.2             gtable_0.2.0                zlibbioc_1.24.0            
 [43] XVector_0.18.0              GetoptLong_0.1.6            DelayedArray_0.4.1          shape_1.4.4                 BiocGenerics_0.24.0         scales_0.5.0               
 [49] DESeq_1.30.0                DBI_1.0.0                   edgeR_3.20.9                ggthemes_3.5.0              Rcpp_0.12.17                xtable_1.8-2               
 [55] progress_1.1.2              cmprsk_2.2-7                foreign_0.8-70              bit_1.1-13                  matlab_1.0.2                km.ci_0.5-2                
 [61] stats4_3.4.4                htmlwidgets_1.2             httr_1.3.1                  RColorBrewer_1.1-2          pkgconfig_2.0.1             XML_3.98-1.11              
 [67] R.methodsS3_1.7.1           locfit_1.5-9.1              tidyselect_0.2.4            rlang_0.2.1                 reshape2_1.4.3              AnnotationDbi_1.40.0       
 [73] munsell_0.4.3               tools_3.4.4                 downloader_0.4              RSQLite_2.1.1               devtools_1.13.5             broom_0.4.4                
 [79] stringr_1.3.1               yaml_2.1.19                 knitr_1.20                  bit64_0.9-7                 survMisc_0.5.4              purrr_0.2.4                
 [85] bindrcpp_0.2.2              EDASeq_2.12.0               nlme_3.1-137                R.oo_1.22.0                 xml2_1.2.0                  biomaRt_2.34.2             
 [91] compiler_3.4.4              curl_3.2                    tibble_1.4.2                geneplotter_1.56.0          stringi_1.2.2               GenomicFeatures_1.30.3     
 [97] lattice_0.20-35             Matrix_1.2-14               psych_1.8.4                 KMsurv_0.1-5                pillar_1.2.2                GlobalOptions_0.0.13       
[103] bitops_1.0-6                rtracklayer_1.38.3          GenomicRanges_1.30.3        R6_2.2.2                    latticeExtra_0.6-28         hwriter_1.3.2              
[109] RMySQL_0.10.15              ShortRead_1.36.1            gridExtra_2.3               IRanges_2.12.0              codetools_0.2-15            assertthat_0.2.0           
[115] SummarizedExperiment_1.8.1  rjson_0.2.18                withr_2.1.2                 GenomicAlignments_1.14.2    Rsamtools_1.30.0            mnormt_1.5-5               
[121] S4Vectors_0.16.0            GenomeInfoDbData_1.0.0      mgcv_1.8-23                 parallel_3.4.4              hms_0.4.2                   grid_3.4.4                 
[127] tidyr_0.8.0                 git2r_0.21.0                ggpubr_0.1.6                Biobase_2.38.0             

[Melkiades]

That error can be resolved after restarting the R session and it is independent from TCGAbiolinks (it is data.table as you can see. Here, there is a similar problem-solution.

[mbk0asis]

Thanks! It works!

[btbbtzhang]

Hey! The same problem come back again! I did the updates of all packages. My colleague told me that I might need to wait for another day to try it again. Is it because of GDC internet portal unstable???

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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 stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] DO.db_2.9 AnnotationDbi_1.36.2 IRanges_2.8.2 S4Vectors_0.12.2
[5] Biobase_2.34.0 BiocGenerics_0.20.0 TCGAbiolinks_2.9.4 readr_1.1.1
[9] data.table_1.11.4

loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.4-1 rjson_0.2.20
[4] hwriter_1.3.2 class_7.3-14 modeltools_0.2-22
[7] mclust_5.4.1 circlize_0.4.4 XVector_0.14.1
[10] GenomicRanges_1.26.4 GlobalOptions_0.1.0 rstudioapi_0.7
[13] ggpubr_0.1.7 matlab_1.0.2 ggrepel_0.8.0
[16] flexmix_2.3-14 bit64_0.9-7 mvtnorm_1.0-8
[19] xml2_1.2.0 codetools_0.2-15 splines_3.5.0
[22] R.methodsS3_1.7.1 doParallel_1.0.11 DESeq_1.26.0
[25] robustbase_0.93-2 geneplotter_1.52.0 knitr_1.20
[28] jsonlite_1.5 Rsamtools_1.26.2 km.ci_0.5-2
[31] broom_0.5.0 annotate_1.52.1 cluster_2.0.7-1
[34] kernlab_0.9-27 R.oo_1.22.0 compiler_3.5.0
[37] httr_1.3.1 backports_1.1.2 assertthat_0.2.0
[40] Matrix_1.2-14 lazyeval_0.2.1 limma_3.30.13
[43] tools_3.5.0 bindrcpp_0.2.2 gtable_0.2.0
[46] glue_1.3.0 dplyr_0.7.6 ggthemes_4.0.1
[49] ShortRead_1.32.1 Rcpp_0.12.18 trimcluster_0.1-2.1
[52] Biostrings_2.42.1 nlme_3.1-137 rtracklayer_1.34.2
[55] iterators_1.0.10 fpc_2.1-11.1 stringr_1.3.1
[58] rvest_0.3.2 XML_3.98-1.16 dendextend_1.8.0
[61] edgeR_3.16.5 DEoptimR_1.0-8 zoo_1.8-3
[64] zlibbioc_1.20.0 MASS_7.3-49 scales_1.0.0
[67] aroma.light_3.4.0 hms_0.4.2 SummarizedExperiment_1.4.0 [70] RColorBrewer_1.1-2 curl_3.2 ComplexHeatmap_1.12.0
[73] memoise_1.1.0 gridExtra_2.3 KMsurv_0.1-5
[76] ggplot2_3.0.0 downloader_0.4 biomaRt_2.30.0
[79] latticeExtra_0.6-28 stringi_1.2.4 RSQLite_2.1.1
[82] genefilter_1.56.0 foreach_1.4.4 GenomicFeatures_1.26.4
[85] BiocParallel_1.8.2 shape_1.4.4 GenomeInfoDb_1.10.3
[88] rlang_0.2.2 pkgconfig_2.0.2 prabclus_2.2-6
[91] matrixStats_0.54.0 bitops_1.0-6 lattice_0.20-35
[94] purrr_0.2.5 bindr_0.1.1 cmprsk_2.2-7
[97] GenomicAlignments_1.10.1 bit_1.1-14 tidyselect_0.2.4
[100] plyr_1.8.4 magrittr_1.5 R6_2.2.2
[103] DBI_1.0.0 mgcv_1.8-23 pillar_1.3.0
[106] whisker_0.3-2 survival_2.41-3 RCurl_1.95-4.11
[109] nnet_7.3-12 tibble_1.4.2 EDASeq_2.8.0
[112] crayon_1.3.4 survMisc_0.5.5 viridis_0.5.1
[115] GetoptLong_0.1.7 locfit_1.5-9.1 grid_3.5.0
[118] sva_3.22.0 blob_1.1.1 ConsensusClusterPlus_1.38.0 [121] digest_0.6.15 diptest_0.75-7 xtable_1.8-2
[124] tidyr_0.8.1 R.utils_2.7.0 munsell_0.5.0
[127] viridisLite_0.3.0 survminer_0.4.3

Sorry, I think the error may be a little bit different, here is the error:

Error: Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed: URL: https://api.gdc.cancer.gov/legacy/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=7173&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-BRCA%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Simple%20nucleotide%20variation%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Genotypes%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.platform%22,%22value%22:[%22Affymetrix%20SNP%20Array%206.0%22]%7D%7D]%7D&format=JSON error: HTTP error 504.

We will retry to access GDC! Error: lexical error: invalid char in json text.