[Bioc-devel] SPB inconsistencies

Ramos Perez, Marcel M@rce|@R@mo@Perez @end|ng |rom Ro@we||P@rk@org
Mon Mar 4 20:31:16 CET 2019


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

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