On Thu, Jun 3, 2021 at 9:11 AM Shraddha Pai <shraddha....@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 <st...@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....@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 confidentia...{{dropped:11}}
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
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>> contains patient information, please contact the Partners Compliance HelpLine
>> at
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>
>
--
The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline
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