[Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
Shraddha Pai
@hr@ddh@@p@| @end|ng |rom utoronto@c@
Thu Jun 3 15:11:38 CEST 2021
Hi Vincent,
Thank you. This is for a workshop with pre-selected versions of R/BioC, so
I have no control over the release.
Will try redownloading the data. I just found it puzzling that the
identical code works in command-line R (ie started from bash shell) but not
in Rstudio but perhaps they have different ways of caching loaded MAE
objects?
Best,Shraddha
On Wed, Jun 2, 2021 at 4:28 PM Vincent Carey <stvjc using channing.harvard.edu>
wrote:
> You are behind the release and should update. However, with a reasonably
> close
> instance I can't reproduce your error. I had a flaky download at one
> point; you might
> want to reconstitute your brca data.
>
> > brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray", "Methylation_methyl27"), dry.run=FALSE)snapshotDate(): 2020-10-27Working on: BRCA_miRNASeqGene-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading 1 resourcesretrieving 1 resource |===================================================================================| 100%loading from cacheWorking on: BRCA_mRNAArray-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading 1 resourcesretrieving 1 resource |===================================================================================| 100%loading from cacheWorking on: BRCA_RPPAArray-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading 1 resourcesretrieving 1 resource |===================================================================================| 100%loading from cacheWorking on: BRCA_Methylation_methyl27-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cachesee ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheWorking on: BRCA_colData-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheWorking on: BRCA_metadata-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheWorking on: BRCA_sampleMap-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheharmonizing input:
> removing 11654 sampleMap rows not in names(experiments)
> removing 1 colData rownames not in sampleMap 'primary'> brcaA MultiAssayExperiment object of 4 listed
> experiments with user-defined names and respective classes.
> Containing an ExperimentList class object of length 4:
> [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns
> [2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns
> [3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
> [4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns
> Functionality:
> experiments() - obtain the ExperimentList instance
> colData() - the primary/phenotype DataFrame
> sampleMap() - the sample coordination DataFrame
> `$`, `[`, `[[` - extract colData columns, subset, or experiment
> *Format() - convert into a long or wide DataFrame
> assays() - convert ExperimentList to a SimpleList of matrices
> exportClass() - save all data to files> assay(experiments(brca)[[4]])<27578 x 343> matrix of class DelayedMatrix and type "double":
> TCGA-A1-A0SD-01A-11D-A112-05 ... TCGA-E2-A15T-01A-11D-A112-05
> cg00000292 0.60555263 . 0.25951246
> cg00002426 0.06197412 . 0.04144839
> cg00003994 0.33345006 . 0.34969161
> cg00005847 0.67217034 . 0.83666264
> cg00006414 NA . NA
> ... . . .
> cg27657283 0.04196141 . 0.03385843
> cg27661264 0.51756951 . 0.47593756
> cg27662379 0.01078112 . 0.01157093
> cg27662877 0.03112835 . 0.02603354
> cg27665659 0.01072116 . 0.01756740> sessionInfo()R version 4.0.3 (2020-10-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 20.04 LTS
>
> Matrix products: default
> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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=C
> [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] rhdf5_2.34.0 curatedTCGAData_1.12.1 MultiAssayExperiment_1.16.0
> [4] SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0
> [7] GenomeInfoDb_1.26.7 IRanges_2.24.1 S4Vectors_0.28.1
> [10] BiocGenerics_0.36.1 MatrixGenerics_1.2.1 matrixStats_0.59.0
> [13] httr_1.4.2 magrittr_2.0.1 AnVIL_1.5.0
> [16] dplyr_1.0.6 BiocManager_1.30.15
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-7 bit64_4.0.5
> [3] rprojroot_2.0.2 tools_4.0.3
> [5] R6_2.5.0 HDF5Array_1.18.1
> [7] DBI_1.1.1 colorspace_2.0-1
> [9] rhdf5filters_1.2.1 withr_2.4.2
> [11] tidyselect_1.1.1 prettyunits_1.1.1
> [13] processx_3.5.2 bit_4.0.4
> [15] curl_4.3.1 compiler_4.0.3
> [17] cli_2.5.0 formatR_1.11
> [19] DelayedArray_0.16.3 scales_1.1.1
> [21] callr_3.7.0 rappdirs_0.3.3
> [23] rapiclient_0.1.3 digest_0.6.27
> [25] XVector_0.30.0 pkgconfig_2.0.3
> [27] htmltools_0.5.1.1 dbplyr_2.1.1
> [29] fastmap_1.1.0 rlang_0.4.11
> [31] rstudioapi_0.13 RSQLite_2.2.7
> [33] shiny_1.6.0 generics_0.1.0
> [35] jsonlite_1.7.2 RCurl_1.98-1.3
> [37] GenomeInfoDbData_1.2.4 futile.logger_1.4.3
> [39] Matrix_1.3-2 Rcpp_1.0.6
> [41] munsell_0.5.0 Rhdf5lib_1.12.1
> [43] lifecycle_1.0.0 yaml_2.2.1
> [45] zlibbioc_1.36.0 pkgbuild_1.2.0
> [47] BiocFileCache_1.14.0 AnnotationHub_2.22.1
> [49] grid_4.0.3 blob_1.2.1
> [51] promises_1.2.0.1 ExperimentHub_1.16.1
> [53] crayon_1.4.1 lattice_0.20-41
> [55] ps_1.6.0 pillar_1.6.1
> [57] futile.options_1.0.1 glue_1.4.2
> [59] BiocVersion_3.12.0 lambda.r_1.2.4
> [61] remotes_2.3.0 vctrs_0.3.8
> [63] httpuv_1.6.1 gtable_0.3.0
> [65] purrr_0.3.4 tidyr_1.1.3
> [67] assertthat_0.2.1 cachem_1.0.5
> [69] ggplot2_3.3.3 xfun_0.23
> [71] mime_0.10 xtable_1.8-4
> [73] later_1.2.0 tibble_3.1.2
> [75] tinytex_0.32 AnnotationDbi_1.52.0
> [77] memoise_2.0.0 ellipsis_0.3.2
> [79] interactiveDisplayBase_1.28.0
>
>
> On Wed, Jun 2, 2021 at 3:37 PM Shraddha Pai <shraddha.pai using utoronto.ca>
> wrote:
>
>> Hello BioC community,
>>
>> Calling assays() on a SummarizedExperiment object has suddenly started
>> giving me this error in Rstudio but not on command-line R. I have been
>> trying to solve this for a few hours without luck and any help would be
>> great. sessionInfo() output below and this is Rstudio 1.4.
>>
>> Thanks,Shraddha
>>
>> Browse[1]> brcaA MultiAssayExperiment object of 4 listed
>> experiments with user-defined names and respective classes.
>> Containing an ExperimentList class object of length 4:
>> [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows
>> and 166 columns
>> [2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and
>> 453 columns
>> [3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 362
>> columns
>> [4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with
>> 27578 rows and 261 columns
>> Functionality:
>> experiments() - obtain the ExperimentList instance
>> colData() - the primary/phenotype DataFrame
>> sampleMap() - the sample coordination DataFrame
>> `$`, `[`, `[[` - extract colData columns, subset, or experiment
>> *Format() - convert into a long or wide DataFrame
>> assays() - convert ExperimentList to a SimpleList of matrices
>> exportClass() - save all data to files
>>
>>
>> Browse[1]> assays(experiments(brca)[[4]])Error in
>> .Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE =
>> "HDF5Array") :
>> failed to open file '/root/.cache/ExperimentHub/661a6f10d826_2122'
>>
>>
>> Browse[2]> experiments(brca)[[4]]class: SummarizedExperiment
>> dim: 27578 261
>> metadata(0):
>> assays(1): counts
>> rownames(27578): cg00000292 cg00002426 ... cg27662877 cg27665659
>> rowData names(3): Gene_Symbol Chromosome Genomic_Coordinate
>> colnames(261): TCGA-A1-A0SD-01A-11D-A112-05 TCGA-A2-A04N-01A-11D-A112-05
>> ...
>> TCGA-E2-A15S-01A-11D-A112-05 TCGA-E2-A15T-01A-11D-A112-05
>> colData names(0):
>>
>>
>> > sessionInfo()R version 4.0.5 (2021-03-31)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 20.04.2 LTS
>>
>> Matrix products: default
>> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/
>> libopenblasp-r0.3.8.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=C
>> [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
>> [9] base
>>
>> other attached packages:
>> [1] rhdf5_2.34.0 netDx_1.2.3
>> [3] bigmemory_4.5.36 curatedTCGAData_1.12.1
>> [5] MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0
>> [7] Biobase_2.50.0 GenomicRanges_1.42.0
>> [9] GenomeInfoDb_1.26.7 IRanges_2.24.1
>> [11] S4Vectors_0.28.1 BiocGenerics_0.36.1
>> [13] MatrixGenerics_1.2.1 matrixStats_0.58.0
>>
>> loaded via a namespace (and not attached):
>> [1] uuid_0.1-4 AnnotationHub_2.22.1
>> [3] BiocFileCache_1.14.0 NMF_0.23.0
>> [5] plyr_1.8.6 igraph_1.2.6
>> [7] RCy3_2.10.2 lazyeval_0.2.2
>> [9] splines_4.0.5 entropy_1.3.0
>> [11] BiocParallel_1.24.1 scater_1.18.6
>> [13] rncl_0.8.4 ggplot2_3.3.3
>> [15] gridBase_0.4-7 digest_0.6.27
>> [17] foreach_1.5.1 htmltools_0.5.1.1
>> [19] viridis_0.6.1 fansi_0.4.2
>> [21] magrittr_2.0.1 memoise_2.0.0
>> [23] cluster_2.1.1 doParallel_1.0.16
>> [25] ROCR_1.0-11 limma_3.46.0
>> [27] annotate_1.68.0 R.utils_2.10.1
>> [29] prettyunits_1.1.1 colorspace_2.0-1
>> [31] blob_1.2.1 rappdirs_0.3.3
>> [33] xfun_0.23 dplyr_1.0.6
>> [35] crayon_1.4.1 RCurl_1.98-1.3
>> [37] bigmemory.sri_0.1.3 graph_1.68.0
>> [39] genefilter_1.72.1 phylobase_0.8.10
>> [41] survival_3.2-10 iterators_1.0.13
>> [43] ape_5.5 glue_1.4.2
>> [45] registry_0.5-1 gtable_0.3.0
>> [47] zlibbioc_1.36.0 XVector_0.30.0
>> [49] DelayedArray_0.16.3 BiocSingular_1.6.0
>> [51] kernlab_0.9-29 Rhdf5lib_1.12.1
>> [53] shape_1.4.6 SingleCellExperiment_1.12.0
>> [55] HDF5Array_1.18.1 scales_1.1.1
>> [57] DBI_1.1.1 edgeR_3.32.1
>> [59] rngtools_1.5 Rcpp_1.0.6
>> [61] viridisLite_0.4.0 xtable_1.8-4
>> [63] progress_1.2.2 rsvd_1.0.5
>> [65] bit_4.0.4 glmnet_4.1-1
>> [67] netSmooth_1.10.0 httr_1.4.2
>> [69] RColorBrewer_1.1-2 ellipsis_0.3.2
>> [71] scuttle_1.0.4 pkgconfig_2.0.3
>> [73] XML_3.99-0.6 R.methodsS3_1.8.1
>> [75] dbplyr_2.1.1 locfit_1.5-9.4
>> [77] utf8_1.2.1 RJSONIO_1.3-1.4
>> [79] howmany_0.3-1 tidyselect_1.1.1
>> [81] rlang_0.4.11 softImpute_1.4-1
>> [83] reshape2_1.4.4 later_1.2.0
>> [85] AnnotationDbi_1.52.0 munsell_0.5.0
>> [87] BiocVersion_3.12.0 tools_4.0.5
>> [89] cachem_1.0.5 generics_0.1.0
>> [91] RSQLite_2.2.7 ExperimentHub_1.16.1
>> [93] ade4_1.7-16 evaluate_0.14
>> [95] stringr_1.4.0 fastmap_1.1.0
>> [97] yaml_2.2.1 knitr_1.33
>> [99] bit64_4.0.5 purrr_0.3.4
>> [101] sparseMatrixStats_1.2.1 nlme_3.1-152
>> [103] mime_0.10 R.oo_1.24.0
>> [105] pracma_2.3.3 xml2_1.3.2
>> [107] compiler_4.0.5 beeswarm_0.3.1
>> [109] curl_4.3.1 interactiveDisplayBase_1.28.0
>> [111] tibble_3.1.2 RNeXML_2.4.5
>> [113] stringi_1.6.2 RSpectra_0.16-0
>> [115] lattice_0.20-41 Matrix_1.3-2
>> [117] vctrs_0.3.8 pillar_1.6.1
>> [119] lifecycle_1.0.0 rhdf5filters_1.2.1
>> [121] BiocManager_1.30.15 combinat_0.0-8
>> [123] BiocNeighbors_1.8.2 zinbwave_1.12.0
>> [125] data.table_1.14.0 irlba_2.3.3
>> [127] bitops_1.0-7 httpuv_1.6.1
>> [129] R6_2.5.0 promises_1.2.0.1
>> [131] gridExtra_2.3 vipor_0.4.5
>> [133] codetools_0.2-18 MASS_7.3-53.1
>> [135] assertthat_0.2.1 pkgmaker_0.32.2
>> [137] withr_2.4.2 GenomeInfoDbData_1.2.4
>> [139] locfdr_1.1-8 hms_1.1.0
>> [141] beachmat_2.6.4 grid_4.0.5
>> [143] tidyr_1.1.3 DelayedMatrixStats_1.12.3
>> [145] rmarkdown_2.8 Rtsne_0.15
>> [147] clusterExperiment_2.10.1 shiny_1.6.0
>> [149] ggbeeswarm_0.6.0 tinytex_0.31
>>
>>
>>
>> --
>>
>> *Shraddha Pai, PhD*
>> Principal Investigator
>> shraddhapai.com; @spaiglass on Twitter
>>
>>
>> *Ontario Institute for Cancer Research*
>> MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada
>> M5G
>> 0A3
>> *@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
>> <http://www.oicr.on.ca/>
>>
>>
>>
>> *Collaborate. Translate. Change lives.*
>>
>>
>>
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>>
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