| Back to Build/check report for BioC 3.19 experimental data |
|
This page was generated on 2024-05-16 14:51:31 -0400 (Thu, 16 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| 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: 2024-05-16 11:10:59 -0400 (Thu, 16 May 2024) |
| EndedAt: 2024-05-16 11:33:53 -0400 (Thu, 16 May 2024) |
| EllapsedTime: 1374.3 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 190.352 9.719 220.050
getPCaSummarySamples 25.534 1.546 29.640
getPCaSummarySurv 25.290 1.204 29.033
getPCaSummaryTable 24.683 1.752 29.217
curatedPCaDatasets_abida 17.254 1.008 19.701
curatedPCaDatasets_taylor 13.670 0.888 15.896
curatedPCaDatasets_tcga 13.553 0.843 15.772
getPCa 13.506 0.652 15.573
curatedPCaDatasets_barbieri 12.697 0.723 14.672
curatedPCaDatasets_weiner 11.521 0.828 13.491
curatedPCaDatasets_ren 11.176 0.559 12.820
curatedPCaDatasets_chandran 10.435 0.628 12.101
curatedPCaDatasets_friedrich 10.039 0.744 11.987
curatedPCaDatasets_wang 10.192 0.497 11.793
curatedPCaDatasets_sun 10.121 0.563 11.707
curatedPCaDatasets_kim 9.968 0.555 11.743
curatedPCaDatasets_wallace 9.795 0.503 11.409
curatedPCaDatasets_icgcca 9.584 0.697 11.339
curatedPCaDatasets_kunderfranco 9.697 0.569 11.402
curatedPCaDatasets_igc 9.449 0.532 11.169
curatedPCaDatasets_true 9.039 0.517 10.583
curatedPCaDatasets_barwick 8.379 0.416 10.107
curatedPCaDatasets_baca 4.374 0.260 5.215
* 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
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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
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")$sample_type ==
+ "primary")
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
[1] TRUE
> # Test omitting metastatic samples from Chandran et al.
> all(curatedPCaData::getPCa("chandran", sampletypes = c("primary", "normal")
+ )$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
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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
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
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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
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
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
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
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
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
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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
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
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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
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
247.070 15.591 287.861
curatedPCaData.Rcheck/curatedPCaData-Ex.timings
| name | user | system | elapsed | |
| curatedPCaDatasets_abida | 17.254 | 1.008 | 19.701 | |
| curatedPCaDatasets_baca | 4.374 | 0.260 | 5.215 | |
| curatedPCaDatasets_barbieri | 12.697 | 0.723 | 14.672 | |
| curatedPCaDatasets_barwick | 8.379 | 0.416 | 10.107 | |
| curatedPCaDatasets_chandran | 10.435 | 0.628 | 12.101 | |
| curatedPCaDatasets_friedrich | 10.039 | 0.744 | 11.987 | |
| curatedPCaDatasets_hieronymus | 3.361 | 0.276 | 4.083 | |
| curatedPCaDatasets_icgcca | 9.584 | 0.697 | 11.339 | |
| curatedPCaDatasets_igc | 9.449 | 0.532 | 11.169 | |
| curatedPCaDatasets_kim | 9.968 | 0.555 | 11.743 | |
| curatedPCaDatasets_kunderfranco | 9.697 | 0.569 | 11.402 | |
| curatedPCaDatasets_ren | 11.176 | 0.559 | 12.820 | |
| curatedPCaDatasets_sun | 10.121 | 0.563 | 11.707 | |
| curatedPCaDatasets_taylor | 13.670 | 0.888 | 15.896 | |
| curatedPCaDatasets_tcga | 13.553 | 0.843 | 15.772 | |
| curatedPCaDatasets_true | 9.039 | 0.517 | 10.583 | |
| curatedPCaDatasets_wallace | 9.795 | 0.503 | 11.409 | |
| curatedPCaDatasets_wang | 10.192 | 0.497 | 11.793 | |
| curatedPCaDatasets_weiner | 11.521 | 0.828 | 13.491 | |
| getPCa | 13.506 | 0.652 | 15.573 | |
| getPCaStudies | 0.005 | 0.000 | 0.005 | |
| getPCaSummarySamples | 25.534 | 1.546 | 29.640 | |
| getPCaSummaryStudies | 190.352 | 9.719 | 220.050 | |
| getPCaSummarySurv | 25.290 | 1.204 | 29.033 | |
| getPCaSummaryTable | 24.683 | 1.752 | 29.217 | |
| template_prad | 0.004 | 0.003 | 0.008 | |