##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings curatedPCaData_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedPCaData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘curatedPCaData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getPCa.Rd: MultiAssayExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
getPCaSummaryStudies            208.782 19.315 248.129
getPCaSummarySamples             28.358  2.744  33.741
getPCaSummaryTable               27.156  1.374  30.862
getPCaSummarySurv                27.112  1.410  30.924
curatedPCaDatasets_abida         17.290  1.225  19.698
getPCa                           15.500  1.989  18.682
curatedPCaDatasets_taylor        15.313  1.888  18.445
curatedPCaDatasets_tcga          14.679  2.124  17.953
curatedPCaDatasets_ren           13.171  1.679  15.905
curatedPCaDatasets_barbieri      13.333  0.930  15.397
curatedPCaDatasets_weiner        12.385  1.738  15.089
curatedPCaDatasets_chandran      11.405  1.723  14.142
curatedPCaDatasets_icgcca        10.753  2.169  13.899
curatedPCaDatasets_kunderfranco  11.478  1.444  13.912
curatedPCaDatasets_kim           11.504  1.353  13.860
curatedPCaDatasets_friedrich     10.994  1.807  13.778
curatedPCaDatasets_sun           11.461  1.328  14.005
curatedPCaDatasets_wang          11.006  1.651  13.768
curatedPCaDatasets_wallace       10.852  1.755  14.618
curatedPCaDatasets_igc           10.856  1.082  13.049
curatedPCaDatasets_true           9.499  1.183  11.564
curatedPCaDatasets_barwick        8.861  1.298  10.993
curatedPCaDatasets_baca           4.665  0.551   5.694
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘native_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedPCaData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL curatedPCaData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘curatedPCaData’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (curatedPCaData)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ###
> #
> # Native 'R CMD check' tests run on the 'curatedPCaData'-package
> # Any exceptions will count as a failure for 'R CMD check' run (notably, does 
> # not require 'RUnit' or 'testthat' packages for testing)
> #
> ###
> 
> ##
> # Testing of getPCa main functionality
> ##
> 
> # Test retrieval of TCGA with all assays
> # Get default fetching of a MAE object based on short id
> methods::is(curatedPCaData::getPCa("tcga"), "MultiAssayExperiment")
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
[1] TRUE
> 
> # Test retrieval of Taylor with a pre-specified subset of assays
> # Get fetching of an assay subset
> methods::is(curatedPCaData::getPCa("taylor", assays = c("gex.rma", "cibersort", 
+     "scores")), "MultiAssayExperiment")
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
harmonizing input:
  removing 1350 sampleMap rows not in names(experiments)
  removing 68 colData rownames not in sampleMap 'primary'
[1] TRUE
> 
> # Test a data fetch that should result in an error
> # Test that an error is produced correctly for a study that does not exist
> methods::is(try({curatedPCaData::getPCa("studyname_misspelled", assays = 
+     c("foo", "bar"))}, silent=TRUE), "try-error")
[1] TRUE
> 
> # Test fetching of an assay that does not exist
> # Test that an error is produced correctly for assays that do not exist
> methods::is(try({curatedPCaData::getPCa("tcga", assays = "typo")}, 
+     silent=TRUE), "try-error")
[1] TRUE
> 
> # Test sample subtype subsetting during getPCa
> # Get only primary samples from TCGA
> all(curatedPCaData::getPCa("tcga", sampletypes = "primary")$sample_type == 
+     "primary")
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
[1] TRUE
> # Test omitting metastatic samples from Chandran et al.
> all(curatedPCaData::getPCa("chandran", sampletypes = c("primary", "normal")
+     )$sample_type %in% c("primary", "normal"))
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
[1] TRUE
> 
> ##
> # Testing of supporting summary functions etc
> ##
> 
> # Test fetching of study short ids and that the 19 studies originally available 
> # in Laajala et al. 2013 are retrieved correctly
> # Tested function: curatedPCaData::getPCaStudies
> studies <- curatedPCaData::getPCaStudies()
> all(c("abida", "baca", "barbieri", "barwick", "chandran", "friedrich", 
+     "hieronymus", "icgcca", "igc", "kim", "kunderfranco", "ren", "sun", 
+     "taylor", "tcga", "true", "wallace", "wang", "weiner") %in% studies)
[1] TRUE
> 
> # Fetch MAE objects for further use
> maes <- lapply(studies, FUN=\(id) { curatedPCaData::getPCa(id) })
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved 
        components.
> names(maes) <- studies
> 
> # getPCaSummaryTable should summarize into a character matrix key instances and 
> # percentages for certain values for a given colData metadata variable
> # Tested function: curatedPCaData::getPCaSummaryTable
> inherits(curatedPCaData::getPCaSummaryTable(maes, var.name = "grade_group", 
+     vals=c("<=6", "3+4", "4+3", "7", ">=8")), "matrix")
[1] TRUE
> 
> # getPCaSummaryTable should summarize into a character matrix event counts and 
> # follow-up times for a Surv-like data
> # Tested function: curatedPCaData::getPCaSummarySurv
> inherits(curatedPCaData::getPCaSummarySurv(maes, event.name = 
+     "disease_specific_recurrence_status", 
+     time.name = "days_to_disease_specific_recurrence"), "matrix")
[1] TRUE
> 
> # getPCaSummarySamples should return a list of length 2; first element 
> # containing unique assay names and N counts in each study, and second element 
> # a matrix with GEX/CNA/MUT combinations for overlap
> # Tested function: curatedPCaData::getPCaSummarySamples
> inherits(curatedPCaData::getPCaSummarySamples(maes), "list")
[1] TRUE
> length(curatedPCaData::getPCaSummarySamples(maes)) == 2
[1] TRUE
> 
> # getPCaSummaryStudies should create a verbose character matrix depicting key 
> # characteristics for each study, such as sample counts, platforms, and special 
> # notes to be aware of
> # Tested function: curatedPCaData::getPCaSummaryStudies, 
> # curatedPCaData::getPCaStudies
> inherits(curatedPCaData::getPCaSummaryStudies(maes), "matrix")
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
257.306  13.641 293.525