Re: [Bioc-devel] SPB inconsistencies
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"
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-8LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_1.35.1GenomeInfoDb_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_1.0.0XVector_0.23.0
#> [3] compiler_3.6.0BiocManager_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_1.4.0stringr_1.4.0
#> [27] knitr_1.21grid_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_1.4.5.1stringi_1.3.1
#> [43] RCurl_1.95-4.12
Created on 2019-03-04 by the reprex package
(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 <-
Re: [Bioc-devel] SPB inconsistencies
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-8LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_1.35.1GenomeInfoDb_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_1.0.0XVector_0.23.0
#> [3] compiler_3.6.0BiocManager_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_1.4.0stringr_1.4.0
#> [27] knitr_1.21grid_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_1.4.5.1stringi_1.3.1
#> [43] RCurl_1.95-4.12
Created on 2019-03-04 by the reprex package
(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() -
Re: [Bioc-devel] SPB inconsistencies
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 stats4stats 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_1.4.0edgeR_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
[Bioc-devel] SPB inconsistencies
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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel 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_1.4.0GenomicDataCommons_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_1.1-14curl_3.3 [15] compiler_3.6.0rvest_0.3.2 [17] xml2_1.2.0readr_1.3.1 [19] rappdirs_0.3.1stringr_1.4.0 [21] digest_0.6.18 Rsamtools_1.99.2 [23] rmarkdown_1.11pkgconfig_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_1.1.1promises_1.0.1 [43] ExperimentHub_1.9.1 crayon_1.3.4 [45] lattice_0.20-38 hms_0.4.2 [47] locfit_1.5-9.1knitr_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_1.4.5.1purrr_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]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
