| Back to Build/check report for BioC 3.22 experimental data |
|
This page was generated on 2026-04-02 15:41 -0400 (Thu, 02 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4896 |
| 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 87/435 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| curatedPCaData 1.6.0 (landing page) Teemu Daniel Laajala
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the curatedPCaData package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: curatedPCaData |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings curatedPCaData_1.6.0.tar.gz |
| StartedAt: 2026-04-02 12:11:30 -0400 (Thu, 02 Apr 2026) |
| EndedAt: 2026-04-02 12:36:03 -0400 (Thu, 02 Apr 2026) |
| EllapsedTime: 1472.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedPCaData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings curatedPCaData_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/curatedPCaData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘curatedPCaData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
getPCa.Rd: MultiAssayExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getPCaSummaryStudies 206.038 13.312 236.151
getPCaSummarySamples 28.213 3.040 33.062
getPCaSummarySurv 26.839 0.926 29.620
getPCaSummaryTable 26.162 0.794 29.372
curatedPCaDatasets_taylor 16.715 1.143 18.864
curatedPCaDatasets_abida 16.853 0.708 18.636
curatedPCaDatasets_tcga 14.512 1.454 16.870
getPCa 14.241 1.196 16.439
curatedPCaDatasets_ren 14.210 1.214 16.271
curatedPCaDatasets_barbieri 13.147 1.149 15.626
curatedPCaDatasets_sun 12.157 0.999 13.958
curatedPCaDatasets_kunderfranco 11.856 1.011 13.700
curatedPCaDatasets_icgcca 11.329 1.411 13.487
curatedPCaDatasets_kim 11.316 1.020 13.116
curatedPCaDatasets_igc 11.013 0.947 13.109
curatedPCaDatasets_wallace 10.986 0.918 13.254
curatedPCaDatasets_weiner 11.001 0.860 12.622
curatedPCaDatasets_friedrich 10.828 0.864 12.670
curatedPCaDatasets_wang 10.402 1.059 12.587
curatedPCaDatasets_chandran 10.419 0.736 12.051
curatedPCaDatasets_true 9.507 0.822 11.345
curatedPCaDatasets_barwick 8.374 0.517 9.554
curatedPCaDatasets_baca 4.608 0.255 5.271
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘native_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-data-experiment/meat/curatedPCaData.Rcheck/00check.log’
for details.
curatedPCaData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL curatedPCaData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘curatedPCaData’ ... ** this is package ‘curatedPCaData’ version ‘1.6.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (curatedPCaData)
curatedPCaData.Rcheck/tests/native_tests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ###
> #
> # Native 'R CMD check' tests run on the 'curatedPCaData'-package
> # Any exceptions will count as a failure for 'R CMD check' run (notably, does
> # not require 'RUnit' or 'testthat' packages for testing)
> #
> ###
>
> ##
> # Testing of getPCa main functionality
> ##
>
> # Test retrieval of TCGA with all assays
> # Get default fetching of a MAE object based on short id
> methods::is(curatedPCaData::getPCa("tcga"), "MultiAssayExperiment")
Warning: stack imbalance in '::', 6 then 8
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
Error while performing HEAD request.
Proceeding without cache information.
loading from cache
Error while performing HEAD request.
Proceeding without cache information.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
Error while performing HEAD request.
Proceeding without cache information.
loading from cache
Error while performing HEAD request.
Proceeding without cache information.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
Error while performing HEAD request.
Proceeding without cache information.
loading from cache
Error while performing HEAD request.
Proceeding without cache information.
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.
[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
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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")$sample_type ==
+ "primary")
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
components.
[1] TRUE
> # Test omitting metastatic samples from Chandran et al.
> all(curatedPCaData::getPCa("chandran", sampletypes = c("primary", "normal")
+ )$sample_type %in% c("primary", "normal"))
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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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
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Constructing the MultiAssayExperiment object from retrieved
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Constructing the MultiAssayExperiment object from retrieved
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
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Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
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see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
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Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
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Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
see ?curatedPCaData and browseVignettes('curatedPCaData') for documentation
loading from cache
Constructing the MultiAssayExperiment object from retrieved
components.
> names(maes) <- studies
>
> # getPCaSummaryTable should summarize into a character matrix key instances and
> # percentages for certain values for a given colData metadata variable
> # Tested function: curatedPCaData::getPCaSummaryTable
> inherits(curatedPCaData::getPCaSummaryTable(maes, var.name = "grade_group",
+ vals=c("<=6", "3+4", "4+3", "7", ">=8")), "matrix")
[1] TRUE
>
> # getPCaSummaryTable should summarize into a character matrix event counts and
> # follow-up times for a Surv-like data
> # Tested function: curatedPCaData::getPCaSummarySurv
> inherits(curatedPCaData::getPCaSummarySurv(maes, event.name =
+ "disease_specific_recurrence_status",
+ time.name = "days_to_disease_specific_recurrence"), "matrix")
[1] TRUE
>
> # getPCaSummarySamples should return a list of length 2; first element
> # containing unique assay names and N counts in each study, and second element
> # a matrix with GEX/CNA/MUT combinations for overlap
> # Tested function: curatedPCaData::getPCaSummarySamples
> inherits(curatedPCaData::getPCaSummarySamples(maes), "list")
[1] TRUE
> length(curatedPCaData::getPCaSummarySamples(maes)) == 2
[1] TRUE
>
> # getPCaSummaryStudies should create a verbose character matrix depicting key
> # characteristics for each study, such as sample counts, platforms, and special
> # notes to be aware of
> # Tested function: curatedPCaData::getPCaSummaryStudies,
> # curatedPCaData::getPCaStudies
> inherits(curatedPCaData::getPCaSummaryStudies(maes), "matrix")
[1] TRUE
>
>
> proc.time()
user system elapsed
257.687 8.636 348.593
curatedPCaData.Rcheck/curatedPCaData-Ex.timings
| name | user | system | elapsed | |
| curatedPCaDatasets_abida | 16.853 | 0.708 | 18.636 | |
| curatedPCaDatasets_baca | 4.608 | 0.255 | 5.271 | |
| curatedPCaDatasets_barbieri | 13.147 | 1.149 | 15.626 | |
| curatedPCaDatasets_barwick | 8.374 | 0.517 | 9.554 | |
| curatedPCaDatasets_chandran | 10.419 | 0.736 | 12.051 | |
| curatedPCaDatasets_friedrich | 10.828 | 0.864 | 12.670 | |
| curatedPCaDatasets_hieronymus | 3.543 | 0.322 | 4.240 | |
| curatedPCaDatasets_icgcca | 11.329 | 1.411 | 13.487 | |
| curatedPCaDatasets_igc | 11.013 | 0.947 | 13.109 | |
| curatedPCaDatasets_kim | 11.316 | 1.020 | 13.116 | |
| curatedPCaDatasets_kunderfranco | 11.856 | 1.011 | 13.700 | |
| curatedPCaDatasets_ren | 14.210 | 1.214 | 16.271 | |
| curatedPCaDatasets_sun | 12.157 | 0.999 | 13.958 | |
| curatedPCaDatasets_taylor | 16.715 | 1.143 | 18.864 | |
| curatedPCaDatasets_tcga | 14.512 | 1.454 | 16.870 | |
| curatedPCaDatasets_true | 9.507 | 0.822 | 11.345 | |
| curatedPCaDatasets_wallace | 10.986 | 0.918 | 13.254 | |
| curatedPCaDatasets_wang | 10.402 | 1.059 | 12.587 | |
| curatedPCaDatasets_weiner | 11.001 | 0.860 | 12.622 | |
| getPCa | 14.241 | 1.196 | 16.439 | |
| getPCaStudies | 0.005 | 0.000 | 0.006 | |
| getPCaSummarySamples | 28.213 | 3.040 | 33.062 | |
| getPCaSummaryStudies | 206.038 | 13.312 | 236.151 | |
| getPCaSummarySurv | 26.839 | 0.926 | 29.620 | |
| getPCaSummaryTable | 26.162 | 0.794 | 29.372 | |
| template_prad | 0.004 | 0.002 | 0.005 | |