waldronlab/curatedTCGAData

Error reading from connection

Closed this issue · 14 comments

oricel commented

The following is not working for me; any help would be appreciated: I would be happy with downloading only one of the microarray platforms (hg_u133a for example).

curatedTCGAData(diseaseCode = "GBM", assays = "mRNAArray*", dry.run = FALSE)

downloading from ‘https://experimenthub.bioconductor.org/fetch/679’
retrieving 1 resource
|========================================================================================================================| 100%

write error during file appendError: failed to load resource
name: EH679
title: GBM_mRNAArray_huex-20160128
reason: error reading from connection

LiNk-NY commented

Hi @oricel,
Have you tried this recently? It works for me.

Best,
Marcel

lwaldron commented

Also no problem for me, using current bioc-release, see sessionInfo() below. Maybe you had a temporary Internet disruption, or are using an outdated R/Bioc/ExperimentHub? Maybe an old release with the current database could have such problems, but without your sessionInfo() we don't know if that might be the issue.

> x=curatedTCGAData(diseaseCode = "GBM", assays = "mRNAArray*", dry.run = FALSE)
> x
A MultiAssayExperiment object of 3 listed
 experiments with user-defined names and respective classes. 
 Containing an ExperimentList class object of length 3: 
 [1] GBM_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 431 columns 
 [2] GBM_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 502 columns 
 [3] GBM_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 528 columns 
Features: 
 experiments() - obtain the ExperimentList instance 
 colData() - the primary/phenotype DataFrame 
 sampleMap() - the sample availability DataFrame 
 `$`, `[`, `[[` - extract colData columns, subset, or experiment 
 *Format() - convert into a long or wide DataFrame 
 assays() - convert ExperimentList to a SimpleList of matrices
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] curatedTCGAData_1.0.3      MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15                  BiocInstaller_1.28.0         
 [3] AnnotationHub_2.10.1          compiler_3.4.3               
 [5] pillar_1.1.0                  GenomeInfoDb_1.14.0          
 [7] plyr_1.8.4                    XVector_0.18.0               
 [9] bitops_1.0-6                  tools_3.4.3                  
[11] zlibbioc_1.24.0               bit_1.1-12                   
[13] digest_0.6.15                 memoise_1.1.0                
[15] RSQLite_2.0                   tibble_1.4.2                 
[17] lattice_0.20-35               pkgconfig_2.0.1              
[19] rlang_0.2.0                   Matrix_1.2-11                
[21] DBI_0.7                       DelayedArray_0.4.1           
[23] shiny_1.0.5                   curl_3.1                     
[25] yaml_2.1.16                   parallel_3.4.3               
[27] GenomeInfoDbData_1.0.0        httr_1.3.1                   
[29] stringr_1.3.0                 S4Vectors_0.16.0             
[31] IRanges_2.12.0                bit64_0.9-7                  
[33] stats4_3.4.3                  grid_3.4.3                   
[35] shinydashboard_0.6.1          glue_1.2.0                   
[37] Biobase_2.38.0                R6_2.2.2                     
[39] AnnotationDbi_1.40.0          ExperimentHub_1.4.0          
[41] blob_1.1.0                    reshape2_1.4.3               
[43] tidyr_0.8.0                   purrr_0.2.4                  
[45] magrittr_1.5                  matrixStats_0.53.1           
[47] htmltools_0.3.6               BiocGenerics_0.24.0          
[49] GenomicRanges_1.30.2          SummarizedExperiment_1.8.1   
[51] interactiveDisplayBase_1.16.0 mime_0.5                     
[53] xtable_1.8-2                  httpuv_1.3.5                 
[55] stringi_1.1.6                 RCurl_1.95-4.10              
>
oricel commented
oricel commented
oricel commented
oricel commented
LiNk-NY commented

Hi Orieta, @oricel
It looks like you were using the devel version of curatedTCGAData with the release version
of Bioconductor (R version 3.4.3).

It looks like you reinstalled it. Now, be sure to clear your ~/.ExperimentHub cache folder.

Regards,
Marcel

oricel commented
oricel commented

Marcel, the error remains:

I have deleted ~/.ExperimentHub, cleared objects from memory, restarted the R session...

lwaldron commented

I wonder if you can retrieve the ExperimentHub components, like this?

library(ExperimentHub)
eh <- ExperimentHub()
ind <- c(679, 680, 681, 671, 674, 684)
for (i in ind) eh[[i]]
sessionInfo()
oricel commented
oricel commented
lwaldron commented

Hi @oricel, yes, see ?ExperimentHub::setExperimentHubOption, you can either set an environment variable or use an R command like:

setExperimentHubOption("CACHE", "/some/path")

oricel commented