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List: bioc-devel
Subject: Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
From: Marcel Ramos <marcel.ramosperez () roswellpark ! org>
Date: 2021-06-03 18:44:04
Message-ID: d437d431-8984-236b-0859-667d2ac2cdf0 () roswellpark ! org
[Download RAW message or body]
Hi Shraddha,
I am also unable to reproduce this in RStudio Server Version 1.4.1106 using
our Bioc 3.12 Docker container.
There may be some inadvertent version mixing based on the error.
Please make sure the `BiocManager::valid()` is returning `TRUE`.
---
> brca <- curatedTCGAData::curatedTCGAData("BRCA", c("miRNASeqGene",
"mRNAArray", "RPPAArray", "Methylation_methyl27"), dry.run=FALSE)
> brca
A 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
> assays(experiments(brca)[[4]])
List of length 1
names(1): counts
> 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
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-41 \
assertthat_0.2.1 [4] digest_0.6.27 utf8_1.2.1 \
mime_0.10 [7] BiocFileCache_1.14.0 R6_2.5.0 RSQLite_2.2.7
[10] httr_1.4.2 pillar_1.6.1 zlibbioc_1.36.0
[13] rlang_0.4.11 curl_4.3.1 blob_1.2.1
[16] Matrix_1.3-2 AnnotationHub_2.22.1 \
RCurl_1.98-1.3 [19] bit_4.0.4 \
HDF5Array_1.18.1 shiny_1.6.0 [22] DelayedArray_0.16.3 \
compiler_4.0.3 httpuv_1.6.1 [25] pkgconfig_2.0.3 \
htmltools_0.5.1.1 tidyselect_1.1.1 [28] tibble_3.1.2 \
GenomeInfoDbData_1.2.4 interactiveDisplayBase_1.28.0
[31] fansi_0.5.0 withr_2.4.2 crayon_1.4.1
[34] dplyr_1.0.6 dbplyr_2.1.1 later_1.2.0
[37] rhdf5filters_1.2.1 bitops_1.0-7 rappdirs_0.3.3
[40] grid_4.0.3 xtable_1.8-4 lifecycle_1.0.0
[43] DBI_1.1.1 magrittr_2.0.1 cachem_1.0.5
[46] XVector_0.30.0 promises_1.2.0.1 ellipsis_0.3.2
[49] generics_0.1.0 vctrs_0.3.8 Rhdf5lib_1.12.1
[52] tools_4.0.3 bit64_4.0.5 glue_1.4.2
[55] purrr_0.3.4 BiocVersion_3.12.0 fastmap_1.1.0
[58] yaml_2.2.1 AnnotationDbi_1.52.0
ExperimentHub_1.16.1
[61] BiocManager_1.30.15 memoise_2.0.0
---
Best,
Marcel
On 6/3/21 11:21 AM, Vincent Carey wrote:
> On Thu, Jun 3, 2021 at 9:11 AM Shraddha Pai <shraddha.pai@utoronto.ca>
> wrote:
>
> > 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
> >
> I neglected to mention that my transcript was developed in RStudio on
> Terra, with RStudio 1.4.1106, 2389bc24
>
>
> > On Wed, Jun 2, 2021 at 4:28 PM Vincent Carey <stvjc@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@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
> > > >
> > > >
> > > >
> > > > --
> > > >
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Bioconductor Core Team
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