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waldronlab / curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
https://bioconductor.org/packages/curatedTCGAData
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I run into the following problems when using the curatedTCGAData package #32

Closed maggiejiangzhao closed 4 years ago

maggiejiangzhao commented 4 years ago

Hi, I run into the following problems when using the curatedTCGAData package .I want to know the problem is due to the package or our server. Thank you for your help and support. Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : bfcadd() failed; see warnings() In addition: Warning messages: 1: download failed web resource path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’ local file path: ‘/cluster/home/zjiang/.cache/ExperimentHub/137fc55b5bf3e_experimenthub.sqlite3’ reason: An unknown option was passed in to libcurl 2: bfcadd() failed; resource removed rid: BFC5 fpath: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’ reason: download failed

LiNk-NY commented 4 years ago

Hi Maggie, @maggiejiangzhao Can you please provide a minimally reproducible example and include sessionInfo()? Thank you. MR

maggiejiangzhao commented 4 years ago 
  library(dplyr)
  library(ggplot2)
  library(survival)
  library(loose.rock)
  library(futile.logger)
  library(curatedTCGAData)
  library(TCGAutils)
  library(glmSparseNet)
.Last.value <- flog.layout(layout.format('[~l] ~m'))
.Last.value <- loose.rock::show.message(FALSE)
theme_set(ggplot2::theme_minimal())
brca <- curatedTCGAData(diseaseCode = "BRCA", assays = "RNASeq2GeneNorm", FALSE)
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /cluster/apps/R/3.6.1/lib64/R/lib/libRblas.so
LAPACK: /cluster/apps/R/3.6.1/lib64/R/lib/libRlapack.so

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=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] glmSparseNet_1.4.0          glmnet_3.0-1
 [3] Matrix_1.2-17               TCGAutils_1.6.1
 [5] curatedTCGAData_1.8.0       MultiAssayExperiment_1.12.0
 [7] SummarizedExperiment_1.16.0 DelayedArray_0.12.0
 [9] BiocParallel_1.20.0         matrixStats_0.55.0
[11] Biobase_2.46.0              GenomicRanges_1.38.0
[13] GenomeInfoDb_1.22.0         IRanges_2.20.0
[15] S4Vectors_0.24.0            BiocGenerics_0.32.0
[17] futile.logger_1.4.3         loose.rock_1.0.16
[19] survival_3.1-8              ggplot2_3.2.1
[21] dplyr_0.8.3

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                  bit64_0.9-7
 [3] progress_1.2.2                httr_1.4.1
 [5] GenomicDataCommons_1.10.0     tools_3.6.1
 [7] backports_1.1.5               R6_2.4.0
 [9] DBI_1.0.0                     lazyeval_0.2.2
[11] colorspace_1.4-1              withr_2.1.2
[13] tidyselect_0.2.5              prettyunits_1.0.2
[15] bit_1.1-14                    curl_4.2
[17] compiler_3.6.1                rvest_0.3.5
[19] formatR_1.7                   xml2_1.2.2
[21] rtracklayer_1.46.0            scales_1.0.0
[23] readr_1.3.1                   sparsebn_0.1.0
[25] askpass_1.1                   rappdirs_0.3.1
[27] Rsamtools_2.2.1               stringr_1.4.0
[29] digest_0.6.22                 XVector_0.26.0
[31] pkgconfig_2.0.3               htmltools_0.4.0
[33] dbplyr_1.4.2                  fastmap_1.0.1
[35] rlang_0.4.1                   RSQLite_2.1.4
[37] shiny_1.4.0                   shape_1.4.4
[39] jsonlite_1.6                  sparsebnUtils_0.0.7
[41] RCurl_1.95-4.12               magrittr_1.5
[43] GenomeInfoDbData_1.2.2        Rcpp_1.0.2
[45] munsell_0.5.0                 discretecdAlgorithm_0.0.5
[47] stringi_1.4.3                 yaml_2.2.0
[49] zlibbioc_1.32.0               BiocFileCache_1.10.2
[51] AnnotationHub_2.18.0          grid_3.6.1
[53] blob_1.2.0                    promises_1.1.0
[55] forcats_0.4.0                 ExperimentHub_1.12.0
[57] crayon_1.3.4                  lattice_0.20-38
[59] Biostrings_2.54.0             splines_3.6.1
[61] GenomicFeatures_1.38.0        hms_0.5.2
[63] zeallot_0.1.0                 pillar_1.4.2
[65] codetools_0.2-16              biomaRt_2.42.0
[67] futile.options_1.0.1          XML_3.98-1.20
[69] glue_1.3.1                    BiocVersion_3.10.1
[71] lambda.r_1.2.4                BiocManager_1.30.9
[73] foreach_1.4.7                 vctrs_0.2.0
[75] httpuv_1.5.2                  ccdrAlgorithm_0.0.5
[77] gtable_0.3.0                  openssl_1.4.1
[79] purrr_0.3.3                   assertthat_0.2.1
[81] mime_0.7                      xtable_1.8-4
[83] later_1.0.0                   tibble_2.1.3
[85] iterators_1.0.12              GenomicAlignments_1.22.1
[87] AnnotationDbi_1.48.0          memoise_1.1.0
[89] interactiveDisplayBase_1.24.0

Thank you so much. Maggie

LiNk-NY commented 4 years ago

Hi Maggie, @maggiejiangzhao

I was not able to reproduce the issue on a Ubuntu 19.10 machine. I don't think the issue is with the package.

It may be a system issue concerning the curl installation.

You may have a different / older version of curl installed because there's a warning that says: An unknown option was passed in to libcurl

I hope this helps. Best, Marcel

maggiejiangzhao commented 4 years ago

Hi Marcel， Thanks for your answer and I have got that. Best regards. Maggie

------------------ 原始邮件 ------------------ 发件人: "Marcel Ramos"<notifications@github.com>; 发送时间: 2019年12月11日(星期三) 凌晨1:35 收件人: "waldronlab/curatedTCGAData"<curatedTCGAData@noreply.github.com>; 抄送: "蒋小昭"<895736116@qq.com>;"Mention"<mention@noreply.github.com>; 主题: Re: [waldronlab/curatedTCGAData] I run into the following problems when using the curatedTCGAData package (#32)

Hi Maggie, @maggiejiangzhao

I was not able to reproduce the issue on a Ubuntu 19.10 machine. I don't think the issue is with the package.

It may be a system issue concerning the curl installation.

You may have a different / older version of curl installed because there's a warning that says: An unknown option was passed in to libcurl

I hope this helps. Best, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

muyumuge commented 4 years ago

Hi Maggie, Have you addressed this problem?I run into the same problem too. Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : bfcadd() failed; see warnings() 此外: Warning messages: 1: download failed web resource path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’ local file path: ‘C:\Users\muyumuge\AppData\Local\ExperimentHub\ExperimentHub\Cache/b7c45379d8_experimenthub.sqlite3’ reason: Timeout was reached: [experimenthub.bioconductor.org] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received 2: bfcadd() failed; resource removed rid: BFC13 fpath: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’ reason: download failed How did you solve this problem finally? Thank you so much. muyumuge