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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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Error reading from connection #14

Closed oricel closed 6 years ago

oricel commented 6 years ago

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 6 years ago

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

Best, Marcel

lwaldron commented 6 years ago

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 Maybe you had a temporary Internet disruption, or are using an outdated R/Bioc/ExperimentHub?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 6 years ago

Hi Marcel,

Yes, today. Below is my session info.

Thanks! orieta

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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_1.1.12 MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached): [1] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:30 PM, Levi Waldron notifications@github.com wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367405565, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7Ck3p6gRriRQbDbo_Daf1NXvLxpTCnks5tXFLRgaJpZM4SN8gR .

oricel commented 6 years ago

I tried to uninstall and reinstall ExperimentHub and curatedTCGAData, with the same result: here's the new sessionInfo:

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:39 PM, Orieta Celiku orieta.celiku@gmail.com wrote:

Hi Marcel,

Yes, today. Below is my session info.

Thanks! orieta

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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_1.1.12 MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached): [1] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:30 PM, Levi Waldron notifications@github.com wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367405565, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7Ck3p6gRriRQbDbo_Daf1NXvLxpTCnks5tXFLRgaJpZM4SN8gR .

oricel commented 6 years ago

Also, these are the contents of my /home/rstudio/.ExperimentHub:

[rstudio@ncias-d1706-v .ExperimentHub]$ ls -l total 14684 -rw-r--r--. 1 rstudio r 14102528 Feb 21 12:48 679 -rw-r--r--. 1 rstudio r 909312 Feb 21 12:48 experimenthub.sqlite3 -rw-r--r--. 1 rstudio r 23196 Feb 21 12:48 index.rds

On Wed, Feb 21, 2018 at 12:49 PM, Orieta Celiku orieta.celiku@gmail.com wrote:

I tried to uninstall and reinstall ExperimentHub and curatedTCGAData, with the same result: here's the new sessionInfo:

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:39 PM, Orieta Celiku orieta.celiku@gmail.com wrote:

Hi Marcel,

Yes, today. Below is my session info.

Thanks! orieta

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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_1.1.12 MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached): [1] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:30 PM, Levi Waldron notifications@github.com wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367405565, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7Ck3p6gRriRQbDbo_Daf1NXvLxpTCnks5tXFLRgaJpZM4SN8gR .

oricel commented 6 years ago

I should also add that I tried downloading

rppa <- curatedTCGAData(diseaseCode = "GBM", assays = "RPPA*", dry.run = FALSE)

and this works fine.

On Wed, Feb 21, 2018 at 12:52 PM, Orieta Celiku orieta.celiku@gmail.com wrote:

Also, these are the contents of my /home/rstudio/.ExperimentHub:

[rstudio@ncias-d1706-v .ExperimentHub]$ ls -l total 14684 -rw-r--r--. 1 rstudio r 14102528 Feb 21 12:48 679 -rw-r--r--. 1 rstudio r 909312 Feb 21 12:48 experimenthub.sqlite3 -rw-r--r--. 1 rstudio r 23196 Feb 21 12:48 index.rds

On Wed, Feb 21, 2018 at 12:49 PM, Orieta Celiku orieta.celiku@gmail.com wrote:

I tried to uninstall and reinstall ExperimentHub and curatedTCGAData, with the same result: here's the new sessionInfo:

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:39 PM, Orieta Celiku orieta.celiku@gmail.com wrote:

Hi Marcel,

Yes, today. Below is my session info.

Thanks! orieta

sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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_1.1.12 MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached): [1] Biobase_2.38.0 httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [5] AnnotationHub_2.10.1 splines_3.4.3 shiny_1.0.5 DO.db_2.9 [9] interactiveDisplayBase_1.16.0 rvcheck_0.0.9 stats4_3.4.3 blob_1.1.0 [13] GenomeInfoDbData_1.0.0 yaml_2.1.16 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 glue_1.2.0 digest_0.6.15 GenomicRanges_1.30.2 [21] XVector_0.18.0 qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 [25] httpuv_1.3.5 Matrix_1.2-12 plyr_1.8.4 pkgconfig_2.0.1 [29] clusterProfiler_3.6.0 zlibbioc_1.24.0 purrr_0.2.4 xtable_1.8-2 [33] GO.db_3.5.0 scales_0.5.0 BiocParallel_1.12.0 tibble_1.4.2 [37] IRanges_2.12.0 ggplot2_2.2.1 SummarizedExperiment_1.8.1 BiocGenerics_0.24.0 [41] lazyeval_0.2.1 magrittr_1.5 mime_0.5 memoise_1.1.0 [45] DOSE_3.4.0 shinydashboard_0.6.1 BiocInstaller_1.28.0 tools_3.4.3 [49] data.table_1.10.4-3 matrixStats_0.53.1 stringr_1.3.0 S4Vectors_0.16.0 [53] munsell_0.4.3 DelayedArray_0.4.1 AnnotationDbi_1.40.0 compiler_3.4.3 [57] GenomeInfoDb_1.14.0 rlang_0.2.0 grid_3.4.3 RCurl_1.95-4.10 [61] igraph_1.1.2 bitops_1.0-6 ExperimentHub_1.4.0 gtable_0.2.0 [65] DBI_0.7 curl_3.1 reshape2_1.4.3 R6_2.2.2 [69] gridExtra_2.3 knitr_1.20 bit_1.1-12 fastmatch_1.1-0 [73] fgsea_1.4.1 GOSemSim_2.4.1 stringi_1.1.6 parallel_3.4.3 [77] Rcpp_0.12.15

On Wed, Feb 21, 2018 at 12:30 PM, Levi Waldron <notifications@github.com

wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367405565, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7Ck3p6gRriRQbDbo_Daf1NXvLxpTCnks5tXFLRgaJpZM4SN8gR .

LiNk-NY commented 6 years ago

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 6 years ago

Marcel, the error remains:

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

On Wed, Feb 21, 2018 at 3:02 PM, Marcel Ramos notifications@github.com wrote:

Hi Orieta, @oricel https://github.com/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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367452613, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7Ck1z25Z_HW4WfsQIUuAhvScLXZJbUks5tXHY5gaJpZM4SN8gR .

oricel commented 6 years ago

Marcel, the error remains:

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

lwaldron commented 6 years ago

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 6 years ago

Here's the output:

library(ExperimentHub)Loading required package: AnnotationHub Attaching package: ‘AnnotationHub’ The following object is masked from ‘package:Biobase’:

cache

eh <- ExperimentHub() updating metadata: retrieving 1 resource |=============================================================================================================================| 100% write error during file appendCouldn't set synchronous mode: database disk image is malformed Use synchronous = NULL to turn off this warning.Error: database is corrupt; remove it and try again database: ‘/home/rstudio//.ExperimentHub/experimenthub.sqlite3’ reason: database disk image is malformed > eh <- ExperimentHub() updating metadata: retrieving 1 resource |=============================================================================================================================| 100% snapshotDate(): 2017-10-30 > ind <- c(679, 680, 681, 671, 674, 684)

for (i in ind) eh[[i]]see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/843’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/844’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/845’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/835’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/838’retrieving 1 resource |=============================================================================================================================| 100% write error during file appendError: failed to load resource name: EH838 title: OV_mRNAArray_TX_ht_hg_u133a-20160128 reason: error reading from connection> sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C 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] ExperimentHub_1.4.0 AnnotationHub_2.10.1 maftools_1.4.21 bigmemory_4.5.33 [5] bindrcpp_0.2 plyr_1.8.4 SummarizedExperiment_1.8.1 DelayedArray_0.4.1 [9] matrixStats_0.53.1 Biobase_2.38.0 GenomicRanges_1.30.2 GenomeInfoDb_1.14.0 [13] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 RTCGA.clinical_20151101.8.0 [17] RTCGA_1.8.0 survminer_0.4.2 ggpubr_0.1.6 magrittr_1.5 [21] ggplot2_2.2.1 TCGAbiolinks_2.6.12 DT_0.4 TCGAWorkflowData_1.2.1 [25] extrafont_0.17 reshape2_1.4.3 curatedTCGAData_1.0.3 MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached): [1] shinydashboard_0.6.1 R.utils_2.6.0 RSQLite_2.0 AnnotationDbi_1.40.0 [5] htmlwidgets_1.0 grid_3.4.3 BiocParallel_1.12.0 DESeq_1.30.0 [9] munsell_0.4.3 codetools_0.2-15 colorspace_1.3-2 GOSemSim_2.4.1 [13] BiocInstaller_1.28.0 knitr_1.20 DOSE_3.4.0 Rttf2pt1_1.3.5 [17] NMF_0.20.6 slam_0.1-42 GenomeInfoDbData_1.0.0 mnormt_1.5-5 [21] hwriter_1.3.2 KMsurv_0.1-5 bit64_0.9-7 rprojroot_1.3-2 [25] changepoint_2.2.2 downloader_0.4 ggthemes_3.4.0 EDASeq_2.12.0 [29] R6_2.2.2 doParallel_1.0.11 locfit_1.5-9.1 bitops_1.0-6 [33] fgsea_1.4.1 assertthat_0.2.0.9000 scales_0.5.0 gtable_0.2.0 [37] sva_3.26.0 rlang_0.2.0 genefilter_1.60.0 cmprsk_2.2-7 [41] GlobalOptions_0.0.12 splines_3.4.3 rtracklayer_1.38.3 extrafontdb_1.0 [45] lazyeval_0.2.1 wordcloud_2.5 selectr_0.3-1 broom_0.4.3 [49] yaml_2.1.16 backports_1.1.2 GenomicFeatures_1.30.3 rsconnect_0.8.5 [53] httpuv_1.3.5 qvalue_2.10.0 clusterProfiler_3.6.0 RMySQL_0.10.13 [57] tools_3.4.3 psych_1.7.8 gridBase_0.4-7 RColorBrewer_1.1-2 [61] Rcpp_0.12.15 progress_1.1.2 zlibbioc_1.24.0 purrr_0.2.4 [65] RCurl_1.95-4.10 prettyunits_1.0.2 GetoptLong_0.1.6 viridis_0.5.0 [69] cowplot_0.9.2 zoo_1.8-1 ggrepel_0.7.0 cluster_2.0.6 [73] data.table_1.10.4-3 DO.db_2.9 circlize_0.4.3 aroma.light_3.8.0 [77] evaluate_0.10.1 hms_0.4.1 mime_0.5 xtable_1.8-2 [81] XML_3.98-1.10 mclust_5.4 gridExtra_2.3 shape_1.4.4 [85] compiler_3.4.3 biomaRt_2.34.2 tibble_1.4.2 R.oo_1.21.0 [89] htmltools_0.3.6 mgcv_1.8-23 tidyr_0.8.0 geneplotter_1.56.0 [93] DBI_0.7 matlab_1.0.2 ComplexHeatmap_1.17.1 ShortRead_1.36.0 [97] Matrix_1.2-12 readr_1.1.1 R.methodsS3_1.7.1 bindr_0.1 [101] igraph_1.1.2 pkgconfig_2.0.1 km.ci_0.5-2 bigmemory.sri_0.1.3 [105] rvcheck_0.0.9 GenomicAlignments_1.14.1 registry_0.5 foreign_0.8-69 [109] xml2_1.2.0 foreach_1.4.4 annotate_1.56.1 rngtools_1.2.4 [113] pkgmaker_0.22 XVector_0.18.0 rvest_0.3.2 stringr_1.3.0 [117] VariantAnnotation_1.24.5 digest_0.6.15 ConsensusClusterPlus_1.42.0 Biostrings_2.46.0 [121] rmarkdown_1.8 fastmatch_1.1-0 survMisc_0.5.4 edgeR_3.20.8 [125] curl_3.1 shiny_1.0.5 Rsamtools_1.30.0 rjson_0.2.15 [129] nlme_3.1-131.1 jsonlite_1.5 viridisLite_0.3.0 limma_3.34.8 [133] BSgenome_1.46.0 pillar_1.1.0 lattice_0.20-35 httr_1.3.1 [137] survival_2.41-3 GO.db_3.5.0 interactiveDisplayBase_1.16.0 glue_1.2.0 [141] iterators_1.0.9 bit_1.1-12 stringi_1.1.6 blob_1.1.0 [145] latticeExtra_0.6-28 memoise_1.1.0 dplyr_0.7.4

On Thu, Feb 22, 2018 at 10:25 AM, Levi Waldron notifications@github.com wrote:

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()

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367715965, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7CkxqN3XLfzCw22zOZ1G3hyi1boZDBks5tXYbzgaJpZM4SN8gR .

oricel commented 6 years ago

I think I might have found the problem: there was not enough disk space in the default location of .ExperimentHub. Is there a way to specify a different path for this directory?

On Thu, Feb 22, 2018 at 10:56 AM, Orieta Celiku orieta.celiku@gmail.com wrote:

Here's the output:

library(ExperimentHub)Loading required package: AnnotationHub Attaching package: ‘AnnotationHub’ The following object is masked from ‘package:Biobase’:

cache

eh <- ExperimentHub() updating metadata: retrieving 1 resource |=========================================================== ==================================================================| 100% write error during file appendCouldn't set synchronous mode: database disk image is malformed Use synchronous = NULL to turn off this warning.Error: database is corrupt; remove it and try again database: ‘/home/rstudio//. ExperimentHub/experimenthub.sqlite3’ reason: database disk image is malformed > eh <- ExperimentHub() updating metadata: retrieving 1 resource |=========================================================== ==================================================================| 100% snapshotDate(): 2017-10-30 > ind <- c(679, 680, 681, 671, 674, 684)

for (i in ind) eh[[i]]see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/843’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/844’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/845’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/835’retrieving 1 resource |=============================================================================================================================| 100% see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading from ‘https://experimenthub.bioconductor.org/fetch/838’retrieving 1 resource |=============================================================================================================================| 100% write error during file appendError: failed to load resource name: EH838 title: OV_mRNAArray_TX_ht_hg_u133a-20160128 reason: error reading from connection> sessionInfo()R version 3.4.3 (2017-11-30) 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 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C 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] ExperimentHub_1.4.0 AnnotationHub_2.10.1 maftools_1.4.21 bigmemory_4.5.33 [5] bindrcpp_0.2 plyr_1.8.4 SummarizedExperiment_1.8.1 DelayedArray_0.4.1 [9] matrixStats_0.53.1 Biobase_2.38.0 GenomicRanges_1.30.2 GenomeInfoDb_1.14.0 [13] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 RTCGA.clinical_20151101.8.0 [17] RTCGA_1.8.0 survminer_0.4.2 ggpubr_0.1.6 magrittr_1.5 [21] ggplot2_2.2.1 TCGAbiolinks_2.6.12 DT_0.4 TCGAWorkflowData_1.2.1 [25] extrafont_0.17 reshape2_1.4.3 curatedTCGAData_1.0.3 MultiAssayExperiment_1.4.9

loaded via a namespace (and not attached): [1] shinydashboard_0.6.1 R.utils_2.6.0 RSQLite_2.0 AnnotationDbi_1.40.0 [5] htmlwidgets_1.0 grid_3.4.3 BiocParallel_1.12.0 DESeq_1.30.0 [9] munsell_0.4.3 codetools_0.2-15 colorspace_1.3-2 GOSemSim_2.4.1 [13] BiocInstaller_1.28.0 knitr_1.20 DOSE_3.4.0 Rttf2pt1_1.3.5 [17] NMF_0.20.6 slam_0.1-42 GenomeInfoDbData_1.0.0 mnormt_1.5-5 [21] hwriter_1.3.2 KMsurv_0.1-5 bit64_0.9-7 rprojroot_1.3-2 [25] changepoint_2.2.2 downloader_0.4 ggthemes_3.4.0 EDASeq_2.12.0 [29] R6_2.2.2 doParallel_1.0.11 locfit_1.5-9.1 bitops_1.0-6 [33] fgsea_1.4.1 assertthat_0.2.0.9000 scales_0.5.0 gtable_0.2.0 [37] sva_3.26.0 rlang_0.2.0 genefilter_1.60.0 cmprsk_2.2-7 [41] GlobalOptions_0.0.12 splines_3.4.3 rtracklayer_1.38.3 extrafontdb_1.0 [45] lazyeval_0.2.1 wordcloud_2.5 selectr_0.3-1 broom_0.4.3 [49] yaml_2.1.16 backports_1.1.2 GenomicFeatures_1.30.3 rsconnect_0.8.5 [53] httpuv_1.3.5 qvalue_2.10.0 clusterProfiler_3.6.0 RMySQL_0.10.13 [57] tools_3.4.3 psych_1.7.8 gridBase_0.4-7 RColorBrewer_1.1-2 [61] Rcpp_0.12.15 progress_1.1.2 zlibbioc_1.24.0 purrr_0.2.4 [65] RCurl_1.95-4.10 prettyunits_1.0.2 GetoptLong_0.1.6 viridis_0.5.0 [69] cowplot_0.9.2 zoo_1.8-1 ggrepel_0.7.0 cluster_2.0.6 [73] data.table_1.10.4-3 DO.db_2.9 circlize_0.4.3 aroma.light_3.8.0 [77] evaluate_0.10.1 hms_0.4.1 mime_0.5 xtable_1.8-2 [81] XML_3.98-1.10 mclust_5.4 gridExtra_2.3 shape_1.4.4 [85] compiler_3.4.3 biomaRt_2.34.2 tibble_1.4.2 R.oo_1.21.0 [89] htmltools_0.3.6 mgcv_1.8-23 tidyr_0.8.0 geneplotter_1.56.0 [93] DBI_0.7 matlab_1.0.2 ComplexHeatmap_1.17.1 ShortRead_1.36.0 [97] Matrix_1.2-12 readr_1.1.1 R.methodsS3_1.7.1 bindr_0.1 [101] igraph_1.1.2 pkgconfig_2.0.1 km.ci_0.5-2 bigmemory.sri_0.1.3 [105] rvcheck_0.0.9 GenomicAlignments_1.14.1 registry_0.5 foreign_0.8-69 [109] xml2_1.2.0 foreach_1.4.4 annotate_1.56.1 rngtools_1.2.4 [113] pkgmaker_0.22 XVector_0.18.0 rvest_0.3.2 stringr_1.3.0 [117] VariantAnnotation_1.24.5 digest_0.6.15 ConsensusClusterPlus_1.42.0 Biostrings_2.46.0 [121] rmarkdown_1.8 fastmatch_1.1-0 survMisc_0.5.4 edgeR_3.20.8 [125] curl_3.1 shiny_1.0.5 Rsamtools_1.30.0 rjson_0.2.15 [129] nlme_3.1-131.1 jsonlite_1.5 viridisLite_0.3.0 limma_3.34.8 [133] BSgenome_1.46.0 pillar_1.1.0 lattice_0.20-35 httr_1.3.1 [137] survival_2.41-3 GO.db_3.5.0 interactiveDisplayBase_1.16.0 glue_1.2.0 [141] iterators_1.0.9 bit_1.1-12 stringi_1.1.6 blob_1.1.0 [145] latticeExtra_0.6-28 memoise_1.1.0 dplyr_0.7.4

On Thu, Feb 22, 2018 at 10:25 AM, Levi Waldron notifications@github.com wrote:

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()

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-367715965, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7CkxqN3XLfzCw22zOZ1G3hyi1boZDBks5tXYbzgaJpZM4SN8gR .

lwaldron commented 6 years ago

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 6 years ago

Thank you, this worked. Please feel free to close this.

On Tue, Feb 27, 2018 at 12:14 AM, Levi Waldron notifications@github.com wrote:

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

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedTCGAData/issues/14#issuecomment-368750050, or mute the thread https://github.com/notifications/unsubscribe-auth/AL7Ck0DkfkcTgaF1eLoXXv2ZJm8ChuRUks5tY48xgaJpZM4SN8gR .