Closed lwaldron closed 6 years ago
Maybe jumping the gun here, but:
> curatedTCGAData("ACC", dry.run=FALSE, assays=c("CNASNP", "Mutation", "RPPAArray")) snapshotDate(): 2017-10-12 snapshotDate(): 2017-10-12 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation loading from cache ‘/Users/lwaldron//.ExperimentHub/558’ snapshotDate(): 2017-10-12 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation downloading from ‘https://experimenthub.bioconductor.org/fetch/566’ retrieving 1 resource |===========================================================================================================| 100% snapshotDate(): 2017-10-12 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation downloading from ‘https://experimenthub.bioconductor.org/fetch/568’ retrieving 1 resource |===========================================================================================================| 100% Loading required package: RaggedExperiment in method for ‘coerce’ with signature ‘"RangedRaggedAssay","RaggedExperiment"’: no definition for class “RaggedExperiment” snapshotDate(): 2017-10-12 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation downloading from ‘https://experimenthub.bioconductor.org/fetch/560’ retrieving 1 resource |===========================================================================================================| 100% snapshotDate(): 2017-10-12 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation downloading from ‘https://experimenthub.bioconductor.org/fetch/563’ retrieving 1 resource |===========================================================================================================| 100% snapshotDate(): 2017-10-12 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation downloading from ‘https://experimenthub.bioconductor.org/fetch/569’ retrieving 1 resource |===========================================================================================================| 100% Error in (function (experiments = ExperimentList(), colData = S4Vectors::DataFrame(), : unused arguments (`ACC_colData-20160128` = <S4 object of class "DataFrame">, `ACC_metadata-20160128` = list(buildDate = 1506452819.92055, cancerCode = "ACC", runDate = "20160128", analyzeDate = "20160128", session_info = list(platform = list(version = "R Under development (unstable) (2017-04-12 r72509)", system = "x86_64, linux-gnu", ui = "X11", language = "(EN)", collate = "en_US.UTF-8", tz = "posixrules", date = "2017-09-26"), packages = list(package = c("AnnotationDbi", "AnnotationForge", "AnnotationHub", "AnnotationHubData", "assertthat", "base", "bindr", "bindrcpp", "Biobase", "BiocGenerics", "BiocInstaller", "BiocParallel", "biocViews", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cellranger", "compiler", "data.table", "datasets", "DBI", "DelayedArray", "devtools", "digest", "dplyr", "futile.logger", "futile.options", "GenomeInfoDb", "GenomeInfoDbData", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GEOquery", "glue", "graph", "graphics", "grD In addition: Warning messages: 1: database may not be current database: ‘/Users/lwaldron//.ExperimentHub/experimenthub.sqlite3’ reason: Timeout was reached: SSLRead() return error -9806
This was fixed here: 617311d6f5ecd78b03ab3d39b66fd03a4bd92470. Thanks, Marcel
FWIW, The package tests will fail until Lori can update the datasets on ExperimentHub.
Maybe jumping the gun here, but: