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