Teemu Daniel Laajala
| Snapshot Date: 2024-07-11 07:30 -0400 (Thu, 11 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/curatedPCaData |
| git_branch: devel |
| git_last_commit: bd9b303 |
| git_last_commit_date: 2024-05-28 16:50:36 -0400 (Tue, 28 May 2024) |
| Back to Build/check report for BioC 3.20 experimental data |
|
This page was generated on 2024-07-11 14:51 -0400 (Thu, 11 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4675 |
| 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 83/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| curatedPCaData 1.1.1 (landing page) Teemu Daniel Laajala
| nebbiolo2 | Linux (Ubuntu 22.04.3 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: 1.1.1 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings curatedPCaData_1.1.1.tar.gz |
| StartedAt: 2024-07-11 11:08:08 -0400 (Thu, 11 Jul 2024) |
| EndedAt: 2024-07-11 11:32:42 -0400 (Thu, 11 Jul 2024) |
| EllapsedTime: 1473.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedPCaData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings curatedPCaData_1.1.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/curatedPCaData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.1.1’
* 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 209.870 15.215 243.925
getPCaSummarySamples 30.212 2.166 35.045
getPCaSummaryTable 26.774 1.396 30.762
getPCaSummarySurv 26.718 1.221 30.405
curatedPCaDatasets_abida 17.487 1.148 19.985
curatedPCaDatasets_taylor 16.470 1.668 19.349
getPCa 16.122 1.408 18.775
curatedPCaDatasets_tcga 15.831 1.259 18.217
curatedPCaDatasets_ren 13.345 1.317 15.792
curatedPCaDatasets_barbieri 13.248 1.183 15.771
curatedPCaDatasets_weiner 13.036 1.160 15.112
curatedPCaDatasets_sun 11.577 1.052 13.740
curatedPCaDatasets_wang 11.355 0.832 13.327
curatedPCaDatasets_kim 10.992 0.849 12.788
curatedPCaDatasets_kunderfranco 10.955 0.876 12.841
curatedPCaDatasets_wallace 10.806 0.837 13.830
curatedPCaDatasets_friedrich 10.827 0.804 12.641
curatedPCaDatasets_icgcca 10.583 0.580 12.066
curatedPCaDatasets_true 9.992 0.764 11.659
curatedPCaDatasets_igc 10.424 0.321 11.757
curatedPCaDatasets_chandran 9.931 0.636 11.565
curatedPCaDatasets_barwick 8.146 0.628 9.556
curatedPCaDatasets_baca 4.540 0.408 5.386
* 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: OK
curatedPCaData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL curatedPCaData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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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")$sample_type ==
+ "primary")
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
[1] TRUE
> # Test omitting metastatic samples from Chandran et al.
> all(curatedPCaData::getPCa("chandran", sampletypes = c("primary", "normal")
+ )$sample_type %in% c("primary", "normal"))
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for 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
263.496 18.312 304.577
curatedPCaData.Rcheck/curatedPCaData-Ex.timings
| name | user | system | elapsed | |
| curatedPCaDatasets_abida | 17.487 | 1.148 | 19.985 | |
| curatedPCaDatasets_baca | 4.540 | 0.408 | 5.386 | |
| curatedPCaDatasets_barbieri | 13.248 | 1.183 | 15.771 | |
| curatedPCaDatasets_barwick | 8.146 | 0.628 | 9.556 | |
| curatedPCaDatasets_chandran | 9.931 | 0.636 | 11.565 | |
| curatedPCaDatasets_friedrich | 10.827 | 0.804 | 12.641 | |
| curatedPCaDatasets_hieronymus | 3.522 | 0.320 | 4.199 | |
| curatedPCaDatasets_icgcca | 10.583 | 0.580 | 12.066 | |
| curatedPCaDatasets_igc | 10.424 | 0.321 | 11.757 | |
| curatedPCaDatasets_kim | 10.992 | 0.849 | 12.788 | |
| curatedPCaDatasets_kunderfranco | 10.955 | 0.876 | 12.841 | |
| curatedPCaDatasets_ren | 13.345 | 1.317 | 15.792 | |
| curatedPCaDatasets_sun | 11.577 | 1.052 | 13.740 | |
| curatedPCaDatasets_taylor | 16.470 | 1.668 | 19.349 | |
| curatedPCaDatasets_tcga | 15.831 | 1.259 | 18.217 | |
| curatedPCaDatasets_true | 9.992 | 0.764 | 11.659 | |
| curatedPCaDatasets_wallace | 10.806 | 0.837 | 13.830 | |
| curatedPCaDatasets_wang | 11.355 | 0.832 | 13.327 | |
| curatedPCaDatasets_weiner | 13.036 | 1.160 | 15.112 | |
| getPCa | 16.122 | 1.408 | 18.775 | |
| getPCaStudies | 0.006 | 0.000 | 0.006 | |
| getPCaSummarySamples | 30.212 | 2.166 | 35.045 | |
| getPCaSummaryStudies | 209.870 | 15.215 | 243.925 | |
| getPCaSummarySurv | 26.718 | 1.221 | 30.405 | |
| getPCaSummaryTable | 26.774 | 1.396 | 30.762 | |
| template_prad | 0.006 | 0.000 | 0.006 | |