Back to Build/check report for BioC 3.21 experimental data |
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This page was generated on 2025-08-14 15:01 -0400 (Thu, 14 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 85/432 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
curatedPCaData 1.4.0 (landing page) Teemu Daniel Laajala
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the curatedPCaData package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: curatedPCaData |
Version: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2025-08-14 12:07:47 -0400 (Thu, 14 Aug 2025) |
EndedAt: 2025-08-14 12:31:31 -0400 (Thu, 14 Aug 2025) |
EllapsedTime: 1424.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: curatedPCaData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedPCaData.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘curatedPCaData/DESCRIPTION’ ... OK * this is package ‘curatedPCaData’ version ‘1.4.0’ * 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 202.108 10.760 232.376 getPCaSummarySamples 27.193 1.597 31.247 getPCaSummarySurv 27.106 1.447 30.892 getPCaSummaryTable 26.449 1.360 29.961 curatedPCaDatasets_abida 17.894 2.455 21.525 curatedPCaDatasets_taylor 15.188 0.770 17.534 getPCa 13.877 0.820 15.738 curatedPCaDatasets_tcga 13.904 0.781 15.997 curatedPCaDatasets_barbieri 13.178 0.882 15.087 curatedPCaDatasets_ren 12.786 0.609 15.044 curatedPCaDatasets_sun 11.574 0.606 13.265 curatedPCaDatasets_kim 11.514 0.606 13.282 curatedPCaDatasets_weiner 11.284 0.793 13.164 curatedPCaDatasets_kunderfranco 11.276 0.532 12.713 curatedPCaDatasets_wallace 10.873 0.659 12.563 curatedPCaDatasets_friedrich 10.909 0.565 12.369 curatedPCaDatasets_icgcca 10.531 0.604 12.138 curatedPCaDatasets_igc 10.534 0.545 11.944 curatedPCaDatasets_wang 10.286 0.758 12.074 curatedPCaDatasets_chandran 10.153 0.633 11.970 curatedPCaDatasets_true 9.248 0.492 10.551 curatedPCaDatasets_barwick 8.014 0.479 9.294 curatedPCaDatasets_baca 4.698 0.378 5.823 * 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.
curatedPCaData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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’ ... ** this is package ‘curatedPCaData’ version ‘1.4.0’ ** 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)
curatedPCaData.Rcheck/tests/native_tests.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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 264.074 14.490 299.082
curatedPCaData.Rcheck/curatedPCaData-Ex.timings
name | user | system | elapsed | |
curatedPCaDatasets_abida | 17.894 | 2.455 | 21.525 | |
curatedPCaDatasets_baca | 4.698 | 0.378 | 5.823 | |
curatedPCaDatasets_barbieri | 13.178 | 0.882 | 15.087 | |
curatedPCaDatasets_barwick | 8.014 | 0.479 | 9.294 | |
curatedPCaDatasets_chandran | 10.153 | 0.633 | 11.970 | |
curatedPCaDatasets_friedrich | 10.909 | 0.565 | 12.369 | |
curatedPCaDatasets_hieronymus | 3.471 | 0.241 | 4.428 | |
curatedPCaDatasets_icgcca | 10.531 | 0.604 | 12.138 | |
curatedPCaDatasets_igc | 10.534 | 0.545 | 11.944 | |
curatedPCaDatasets_kim | 11.514 | 0.606 | 13.282 | |
curatedPCaDatasets_kunderfranco | 11.276 | 0.532 | 12.713 | |
curatedPCaDatasets_ren | 12.786 | 0.609 | 15.044 | |
curatedPCaDatasets_sun | 11.574 | 0.606 | 13.265 | |
curatedPCaDatasets_taylor | 15.188 | 0.770 | 17.534 | |
curatedPCaDatasets_tcga | 13.904 | 0.781 | 15.997 | |
curatedPCaDatasets_true | 9.248 | 0.492 | 10.551 | |
curatedPCaDatasets_wallace | 10.873 | 0.659 | 12.563 | |
curatedPCaDatasets_wang | 10.286 | 0.758 | 12.074 | |
curatedPCaDatasets_weiner | 11.284 | 0.793 | 13.164 | |
getPCa | 13.877 | 0.820 | 15.738 | |
getPCaStudies | 0.004 | 0.001 | 0.005 | |
getPCaSummarySamples | 27.193 | 1.597 | 31.247 | |
getPCaSummaryStudies | 202.108 | 10.760 | 232.376 | |
getPCaSummarySurv | 27.106 | 1.447 | 30.892 | |
getPCaSummaryTable | 26.449 | 1.360 | 29.961 | |
template_prad | 0.003 | 0.003 | 0.006 | |