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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings curatedPCaData_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedPCaData.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘curatedPCaData/DESCRIPTION’ ... OK
* this is package ‘curatedPCaData’ version ‘1.4.0’
* 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            207.487 22.128 249.206
getPCaSummarySamples             27.086  2.563  32.004
getPCaSummaryTable               26.681  1.982  31.136
getPCaSummarySurv                26.818  1.479  30.887
curatedPCaDatasets_abida         16.924  1.140  19.388
curatedPCaDatasets_taylor        15.263  1.861  18.331
curatedPCaDatasets_tcga          14.149  1.594  17.085
getPCa                           13.503  1.701  16.514
curatedPCaDatasets_barbieri      13.361  1.402  15.910
curatedPCaDatasets_ren           13.149  1.450  15.702
curatedPCaDatasets_weiner        11.983  1.479  14.459
curatedPCaDatasets_sun           11.978  1.116  14.055
curatedPCaDatasets_kunderfranco  11.569  1.342  13.877
curatedPCaDatasets_kim           11.311  1.056  13.380
curatedPCaDatasets_friedrich     10.927  1.297  13.167
curatedPCaDatasets_wallace       10.459  1.233  12.634
curatedPCaDatasets_igc           10.744  0.925  12.604
curatedPCaDatasets_icgcca        10.396  0.825  12.278
curatedPCaDatasets_wang          10.229  0.728  11.913
curatedPCaDatasets_chandran       9.852  0.815  11.662
curatedPCaDatasets_true           9.353  1.039  11.245
curatedPCaDatasets_barwick        8.297  1.268  10.427
curatedPCaDatasets_baca           4.732  0.489   5.881
* 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-3.21-data-experiment/meat/curatedPCaData.Rcheck/00check.log’
for details.