Back to Build/check report for BioC 3.19 experimental data |
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This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
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 84/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
curatedPCaData 1.0.0 (landing page) Teemu Daniel Laajala
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
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: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings curatedPCaData_1.0.0.tar.gz |
StartedAt: 2024-07-02 11:11:02 -0400 (Tue, 02 Jul 2024) |
EndedAt: 2024-07-02 11:34:20 -0400 (Tue, 02 Jul 2024) |
EllapsedTime: 1398.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: curatedPCaData.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings curatedPCaData_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/curatedPCaData.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘curatedPCaData/DESCRIPTION’ ... OK * this is package ‘curatedPCaData’ version ‘1.0.0’ * 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 ... OK * 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 194.000 10.256 225.600 getPCaSummarySamples 27.586 1.649 31.810 getPCaSummarySurv 26.456 1.199 30.618 getPCaSummaryTable 24.538 1.204 28.437 curatedPCaDatasets_abida 17.294 1.634 20.350 getPCa 14.581 0.960 16.837 curatedPCaDatasets_taylor 14.513 0.840 17.307 curatedPCaDatasets_tcga 14.231 0.711 16.191 curatedPCaDatasets_barbieri 12.751 1.157 15.026 curatedPCaDatasets_weiner 11.564 0.992 13.692 curatedPCaDatasets_sun 11.536 0.520 13.148 curatedPCaDatasets_wallace 11.184 0.600 12.815 curatedPCaDatasets_kim 10.867 0.772 12.929 curatedPCaDatasets_ren 10.865 0.677 12.602 curatedPCaDatasets_wang 10.547 0.692 12.396 curatedPCaDatasets_chandran 10.228 0.835 12.306 curatedPCaDatasets_friedrich 9.796 0.939 11.772 curatedPCaDatasets_true 9.741 0.664 11.405 curatedPCaDatasets_icgcca 9.610 0.728 11.469 curatedPCaDatasets_igc 9.627 0.601 15.852 curatedPCaDatasets_kunderfranco 9.377 0.563 10.983 curatedPCaDatasets_barwick 8.261 0.580 9.814 curatedPCaDatasets_baca 4.333 0.252 5.097 * 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 ... ERROR Error(s) in re-building vignettes: --- re-building ‘overview.Rmd’ using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'studies1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'gleasons1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'groups1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'recurrences1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'os1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'tcgaex'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'ehquery'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'access'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'clinical'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'metadat'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'samplecountsoverlap'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'scores'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. The magick package is required to crop "/home/biocbuild/bbs-3.19-data-experiment/meat/curatedPCaData.Rcheck/vign_test/curatedPCaData/vignettes/overview_files/figure-html/unnamed-chunk-8-1.png" but not available. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-9'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Quitting from lines 512-524 [unnamed-chunk-9] (overview.Rmd) Error: processing vignette 'overview.Rmd' failed with diagnostics: Package 'reshape2' is required for 'longFormat()' conversion --- failed re-building ‘overview.Rmd’ SUMMARY: processing the following file failed: ‘overview.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.19-data-experiment/meat/curatedPCaData.Rcheck/00check.log’ for details.
curatedPCaData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL curatedPCaData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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)
curatedPCaData.Rcheck/tests/native_tests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" 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 249.889 27.431 301.392
curatedPCaData.Rcheck/curatedPCaData-Ex.timings
name | user | system | elapsed | |
curatedPCaDatasets_abida | 17.294 | 1.634 | 20.350 | |
curatedPCaDatasets_baca | 4.333 | 0.252 | 5.097 | |
curatedPCaDatasets_barbieri | 12.751 | 1.157 | 15.026 | |
curatedPCaDatasets_barwick | 8.261 | 0.580 | 9.814 | |
curatedPCaDatasets_chandran | 10.228 | 0.835 | 12.306 | |
curatedPCaDatasets_friedrich | 9.796 | 0.939 | 11.772 | |
curatedPCaDatasets_hieronymus | 3.229 | 0.279 | 3.944 | |
curatedPCaDatasets_icgcca | 9.610 | 0.728 | 11.469 | |
curatedPCaDatasets_igc | 9.627 | 0.601 | 15.852 | |
curatedPCaDatasets_kim | 10.867 | 0.772 | 12.929 | |
curatedPCaDatasets_kunderfranco | 9.377 | 0.563 | 10.983 | |
curatedPCaDatasets_ren | 10.865 | 0.677 | 12.602 | |
curatedPCaDatasets_sun | 11.536 | 0.520 | 13.148 | |
curatedPCaDatasets_taylor | 14.513 | 0.840 | 17.307 | |
curatedPCaDatasets_tcga | 14.231 | 0.711 | 16.191 | |
curatedPCaDatasets_true | 9.741 | 0.664 | 11.405 | |
curatedPCaDatasets_wallace | 11.184 | 0.600 | 12.815 | |
curatedPCaDatasets_wang | 10.547 | 0.692 | 12.396 | |
curatedPCaDatasets_weiner | 11.564 | 0.992 | 13.692 | |
getPCa | 14.581 | 0.960 | 16.837 | |
getPCaStudies | 0.006 | 0.000 | 0.005 | |
getPCaSummarySamples | 27.586 | 1.649 | 31.810 | |
getPCaSummaryStudies | 194.000 | 10.256 | 225.600 | |
getPCaSummarySurv | 26.456 | 1.199 | 30.618 | |
getPCaSummaryTable | 24.538 | 1.204 | 28.437 | |
template_prad | 0.006 | 0.000 | 0.006 | |