[Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
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 at 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.* This message and any attachments may contain confident...{{dropped:26}}