[Bioc-devel] EXTERNAL: Re: SPB inconsistencies
Ramos Perez, Marcel
M@rce|@R@mo@Perez @end|ng |rom Ro@we||P@rk@org
Mon Mar 4 23:31:56 CET 2019
Ah yes, I overwrite the existing resource.
I will look into a temporary workaround to downloading the newer GISTIC
resource when the cached one is stale.
Best,
Marcel
On 3/4/19 3:50 PM, Martin Morgan wrote:
> Thanks Marcel -- when you update this data, do you add a new resource or over-write an existing resource? I think the best practice would be to create a new resource, with updated curateTCGAData package & version bump. Martin
>
> On 3/4/19, 2:31 PM, "Bioc-devel on behalf of Ramos Perez, Marcel" <bioc-devel-bounces using r-project.org on behalf of Marcel.RamosPerez using RoswellPark.org> wrote:
>
> Hi Martin,
>
> I suspect that this is due to caching because I'm unable to reproduce
> including after deleting my hub cache.
>
> hb <- ExperimentHub::ExperimentHub()
> #> snapshotDate(): 2019-01-25
>
> unlink(
> AnnotationHub::hubCache(hb),
> recursive = TRUE,
> force = TRUE
> )
>
> suppressMessages({
> gbm <- curatedTCGAData::curatedTCGAData("GBM",
> assays=c("GISTIC_Peaks", "CNVSNP", "RNASeq2GeneNorm"),
> dry.run=FALSE)
> })
>
> gbm
> #> A MultiAssayExperiment object of 3 listed
> #> experiments with user-defined names and respective classes.
> #> Containing an ExperimentList class object of length 3:
> #> [1] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
> #> [2] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns
> #> [3] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 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 Under development (unstable) (2019-03-04 r76198)
> #> Platform: x86_64-pc-linux-gnu (64-bit)
> #> Running under: Ubuntu 18.10
> #>
> #> Matrix products: default
> #> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
> #> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
> #>
> #> 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] parallel stats4 stats graphics grDevices utils datasets
> #> [8] methods base
> #>
> #> other attached packages:
> #> [1] RaggedExperiment_1.7.4 curatedTCGAData_1.5.8
> #> [3] MultiAssayExperiment_1.9.15 SummarizedExperiment_1.13.0
> #> [5] DelayedArray_0.9.8 BiocParallel_1.17.17
> #> [7] matrixStats_0.54.0 Biobase_2.43.1
> #> [9] GenomicRanges_1.35.1 GenomeInfoDb_1.19.2
> #> [11] IRanges_2.17.4 S4Vectors_0.21.10
> #> [13] BiocGenerics_0.29.1 nvimcom_0.9-72
> #>
> #> loaded via a namespace (and not attached):
> #> [1] Rcpp_1.0.0 XVector_0.23.0
> #> [3] compiler_3.6.0 BiocManager_1.30.4.9003
> #> [5] later_0.8.0 highr_0.7
> #> [7] AnnotationHub_2.15.7 zlibbioc_1.29.0
> #> [9] bitops_1.0-6 tools_3.6.0
> #> [11] digest_0.6.18 bit_1.1-14
> #> [13] lattice_0.20-38 RSQLite_2.1.1
> #> [15] evaluate_0.13 memoise_1.1.0
> #> [17] pkgconfig_2.0.2 Matrix_1.2-15
> #> [19] shiny_1.2.0 DBI_1.0.0
> #> [21] curl_3.3 yaml_2.2.0
> #> [23] xfun_0.5 GenomeInfoDbData_1.2.0
> #> [25] httr_1.4.0 stringr_1.4.0
> #> [27] knitr_1.21 grid_3.6.0
> #> [29] bit64_0.9-7 R6_2.4.0
> #> [31] AnnotationDbi_1.45.0 rmarkdown_1.11
> #> [33] ExperimentHub_1.9.1 blob_1.1.1
> #> [35] magrittr_1.5 promises_1.0.1
> #> [37] htmltools_0.3.6 mime_0.6
> #> [39] interactiveDisplayBase_1.21.0 xtable_1.8-3
> #> [41] httpuv_1.4.5.1 stringi_1.3.1
> #> [43] RCurl_1.95-4.12
>
> Created on 2019-03-04 by the reprex package<https://reprex.tidyverse.org> (v0.2.1)
>
>
>
> Best,
>
> Marcel
>
>
>
> On 2/28/19 4:28 PM, Martin Morgan wrote:
>
> In today's R-devel, I install packages required for the vignette, including CNVRanger's Suggests: packages, and ensure that my installation is valid (modulo some irrelevant packages) via BiocManager::valid().
>
> I then Stangle'd the vignette
>
> cd CNVRanger/vignettes
> R CMD Stange CNVRanger.Rmd
>
> and then in a new R session sourced the vignette code
>
> source("CNVRanger.R", echo=TRUE, max=Inf)
>
> it runs until
>
>
>
> library(curatedTCGAData)
>
>
>
>
>
> suppressMessages(
>
>
> + gbm <- curatedTCGAData("GBM",
> + assays=c("GISTIC_Peaks", "CNVSNP", "RNASeq2GeneNorm"),
> + dry.run=FALSE)
> + )
> |======================================================================| 100%
>
> |======================================================================| 100%
>
> |======================================================================| 100%
>
>
>
>
> gbm
>
>
> A MultiAssayExperiment object of 2 listed
> experiments with user-defined names and respective classes.
> Containing an ExperimentList class object of length 2:
> [1] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
> [2] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 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
>
>
>
> ## ----gisticPeaks---------------------------------------------------------
> peaks <- granges(rowRanges(gbm[["GBM_GISTIC_Peaks-20160128"]]))
>
>
> Error in matrixStats::rowRanges(x, ...) :
> Argument 'x' must be a matrix or a vector.
> In addition: Warning message:
> call dbDisconnect() when finished working with a connection
>
> where the problem is apparent
>
>
>
> gbm[["GBM_GISTIC_Peaks-20160128"]]
>
>
> NULL
>
> The MultiAssayExperiment doesn't contain GBM_GISTIC_Peaks-20160128.
>
> If I try something simpler it also fails...
>
>
>
> curatedTCGAData("GBM", assays = "GISTIC_Peaks", dry.run=FALSE)
>
>
> snapshotDate(): 2019-01-25
> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
> downloading 0 resources
> loading from cache
> '/Users/ma38727//.ExperimentHub/2143'
> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
> downloading 0 resources
> loading from cache
> '/Users/ma38727//.ExperimentHub/671'
> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
> downloading 0 resources
> loading from cache
> '/Users/ma38727//.ExperimentHub/674'
> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
> downloading 0 resources
> loading from cache
> '/Users/ma38727//.ExperimentHub/685'
> harmonizing input:
> removing 6149 sampleMap rows not in names(experiments)
> removing 599 colData rownames not in sampleMap 'primary'
> A MultiAssayExperiment object of 0 listed
> experiments with no user-defined names and respective classes.
> Containing an ExperimentList class object of length 0:
> 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
>
> So perhaps the problem is with the curated* package?
>
> Here's my sessionInfo() (yikes!)
>
>
>
> sessionInfo()
>
>
> R Under development (unstable) (2019-02-28 r76173)
> Platform: x86_64-apple-darwin17.7.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
>
> Matrix products: default
> BLAS: /Users/ma38727/bin/R-devel/lib/libRblas.dylib
> LAPACK: /Users/ma38727/bin/R-devel/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel stats4 stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] ensembldb_2.7.9
> [2] AnnotationFilter_1.7.0
> [3] GenomicFeatures_1.35.7
> [4] AnnotationDbi_1.45.0
> [5] TCGAutils_1.3.20
> [6] curatedTCGAData_1.5.8
> [7] MultiAssayExperiment_1.9.15
> [8] SummarizedExperiment_1.13.0
> [9] DelayedArray_0.9.8
> [10] BiocParallel_1.17.17
> [11] matrixStats_0.54.0
> [12] Biobase_2.43.1
> [13] BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99
> [14] BSgenome.Btaurus.UCSC.bosTau6_1.4.0
> [15] BSgenome_1.51.0
> [16] rtracklayer_1.43.2
> [17] Biostrings_2.51.2
> [18] XVector_0.23.0
> [19] regioneR_1.15.2
> [20] AnnotationHub_2.15.7
> [21] CNVRanger_0.99.18
> [22] RaggedExperiment_1.7.4
> [23] GenomicRanges_1.35.1
> [24] GenomeInfoDb_1.19.2
> [25] IRanges_2.17.4
> [26] S4Vectors_0.21.10
> [27] BiocGenerics_0.29.1
>
> loaded via a namespace (and not attached):
> [1] httr_1.4.0 edgeR_3.25.3
> [3] splines_3.6.0 bit64_0.9-7
> [5] jsonlite_1.6 shiny_1.2.0
> [7] assertthat_0.2.0 statmod_1.4.30
> [9] interactiveDisplayBase_1.21.0 BiocManager_1.30.4
> [11] blob_1.1.1 GenomeInfoDbData_1.2.0
> [13] Rsamtools_1.99.2 yaml_2.2.0
> [15] progress_1.2.0 pillar_1.3.1
> [17] RSQLite_2.1.1 lattice_0.20-38
> [19] limma_3.39.12 glue_1.3.0
> [21] digest_0.6.18 promises_1.0.1
> [23] rvest_0.3.2 htmltools_0.3.6
> [25] httpuv_1.4.5.1 Matrix_1.2-15
> [27] XML_3.98-1.17 pkgconfig_2.0.2
> [29] biomaRt_2.39.3 zlibbioc_1.29.0
> [31] purrr_0.3.0 xtable_1.8-3
> [33] later_0.8.0 tibble_2.0.1
> [35] lazyeval_0.2.1 magrittr_1.5
> [37] crayon_1.3.4 mime_0.6
> [39] memoise_1.1.0 xml2_1.2.0
> [41] tools_3.6.0 prettyunits_1.0.2
> [43] hms_0.4.2 stringr_1.4.0
> [45] locfit_1.5-9.1 compiler_3.6.0
> [47] rlang_0.3.1 grid_3.6.0
> [49] GenomicDataCommons_1.7.3 RCurl_1.95-4.11
> [51] rappdirs_0.3.1 bitops_1.0-6
> [53] ExperimentHub_1.9.1 DBI_1.0.0
> [55] curl_3.3 R6_2.4.0
> [57] GenomicAlignments_1.19.1 dplyr_0.8.0.1
> [59] bit_1.1-14 ProtGenerics_1.15.0
> [61] readr_1.3.1 stringi_1.3.1
> [63] Rcpp_1.0.0 tidyselect_0.2.5
>
>
> On 2/28/19, 2:19 PM, "Bioc-devel on behalf of Ludwig Geistlinger" <bioc-devel-bounces using r-project.org on behalf of Ludwig.Geistlinger using sph.cuny.edu><mailto:bioc-devel-bounces using r-project.orgonbehalfofLudwig.Geistlinger@sph.cuny.edu> wrote:
>
> Hi,
>
>
> According to
>
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html
>
>
> all SPB machines run different snapshots of R-devel with the most recent one (2019-01-22 r76000,
>
> already >1 month outdated) installed on celaya2.
>
>
> I observe two things:
>
>
> 1. My package builds on celaya2, but fails to build on the other SPB machines running older R-devel snapshots.
>
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVRanger/
>
>
> 2. Further, I can't reproduce the SPB built error using a recent R-devel snapshot (2019-02-24 r76155) through the bioconductor/devel_base2 docker container.
>
>
> Can you please advise on how to best proceed from my side? Just wait for the SPB R-devel being updated?
>
>
> > sessionInfo()
>
> R Under development (unstable) (2019-02-24 r76155)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 9 (stretch)
>
> Matrix products: default
> BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
>
> 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=C
> [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] stats4 parallel stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] TCGAutils_1.3.19
> [2] BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99
> [3] BSgenome.Btaurus.UCSC.bosTau6_1.4.0
> [4] BSgenome_1.51.0
> [5] rtracklayer_1.43.1
> [6] Biostrings_2.51.2
> [7] XVector_0.23.0
> [8] regioneR_1.15.2
> [9] BiocStyle_2.11.0
> [10] CNVRanger_0.99.7
> [11] curatedTCGAData_1.5.8
> [12] edgeR_3.25.3
> [13] limma_3.39.12
> [14] RaggedExperiment_1.7.4
> [15] MultiAssayExperiment_1.9.15
> [16] SummarizedExperiment_1.13.0
> [17] DelayedArray_0.9.8
> [18] BiocParallel_1.17.16
> [19] matrixStats_0.54.0
> [20] ensembldb_2.7.9
> [21] AnnotationFilter_1.7.0
> [22] GenomicFeatures_1.35.7
> [23] AnnotationDbi_1.45.0
> [24] Biobase_2.43.1
> [25] GenomicRanges_1.35.1
> [26] GenomeInfoDb_1.19.2
> [27] IRanges_2.17.4
> [28] S4Vectors_0.21.10
> [29] AnnotationHub_2.15.7
> [30] BiocGenerics_0.29.1
>
> loaded via a namespace (and not attached):
> [1] ProtGenerics_1.15.0 bitops_1.0-6
> [3] bit64_0.9-7 progress_1.2.0
> [5] httr_1.4.0 GenomicDataCommons_1.7.3
> [7] tools_3.6.0 R6_2.4.0
> [9] DBI_1.0.0 lazyeval_0.2.1
> [11] tidyselect_0.2.5 prettyunits_1.0.2
> [13] bit_1.1-14 curl_3.3
> [15] compiler_3.6.0 rvest_0.3.2
> [17] xml2_1.2.0 readr_1.3.1
> [19] rappdirs_0.3.1 stringr_1.4.0
> [21] digest_0.6.18 Rsamtools_1.99.2
> [23] rmarkdown_1.11 pkgconfig_2.0.2
> [25] htmltools_0.3.6 rlang_0.3.1
> [27] rstudioapi_0.9.0 RSQLite_2.1.1
> [29] shiny_1.2.0 jsonlite_1.6
> [31] dplyr_0.8.0.1 RCurl_1.95-4.11
> [33] magrittr_1.5 GenomeInfoDbData_1.2.0
> [35] Matrix_1.2-15 Rcpp_1.0.0
> [37] stringi_1.3.1 yaml_2.2.0
> [39] zlibbioc_1.29.0 grid_3.6.0
> [41] blob_1.1.1 promises_1.0.1
> [43] ExperimentHub_1.9.1 crayon_1.3.4
> [45] lattice_0.20-38 hms_0.4.2
> [47] locfit_1.5-9.1 knitr_1.21
> [49] pillar_1.3.1 biomaRt_2.39.2
> [51] XML_3.98-1.17 glue_1.3.0
> [53] evaluate_0.13 BiocManager_1.30.4
> [55] httpuv_1.4.5.1 purrr_0.3.0
> [57] assertthat_0.2.0 xfun_0.5
> [59] mime_0.6 xtable_1.8-3
> [61] later_0.8.0 tibble_2.0.1
> [63] GenomicAlignments_1.19.1 memoise_1.1.0
> [65] interactiveDisplayBase_1.21.0
>
> [[alternative HTML version deleted]]
>
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