##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/curatedPCaData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘1.2.0’
* 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            193.161  6.130 217.086
getPCaSummarySamples             26.954  1.476  31.016
getPCaSummarySurv                25.960  0.686  28.998
getPCaSummaryTable               25.514  0.690  28.428
curatedPCaDatasets_abida         16.648  0.581  18.348
curatedPCaDatasets_taylor        16.454  0.387  19.024
curatedPCaDatasets_tcga          14.524  0.463  16.073
getPCa                           14.280  0.659  16.095
curatedPCaDatasets_ren           14.023  0.308  15.341
curatedPCaDatasets_barbieri      13.135  0.511  14.715
curatedPCaDatasets_sun           12.412  0.296  13.628
curatedPCaDatasets_weiner        11.910  0.770  13.680
curatedPCaDatasets_kunderfranco  11.681  0.276  12.778
curatedPCaDatasets_kim           11.422  0.321  12.736
curatedPCaDatasets_friedrich     11.341  0.331  12.616
curatedPCaDatasets_igc           11.203  0.291  12.402
curatedPCaDatasets_icgcca        11.037  0.367  12.341
curatedPCaDatasets_wang          10.603  0.583  12.595
curatedPCaDatasets_wallace       10.774  0.237  11.919
curatedPCaDatasets_chandran      10.182  0.361  11.581
curatedPCaDatasets_true           9.205  0.207  10.251
curatedPCaDatasets_barwick        7.885  0.215   9.195
curatedPCaDatasets_baca           4.410  0.138   5.001
* 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