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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 4.5.1 (2025-06-13)
* 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 24.04.3 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            202.108 10.760 232.376
getPCaSummarySamples             27.193  1.597  31.247
getPCaSummarySurv                27.106  1.447  30.892
getPCaSummaryTable               26.449  1.360  29.961
curatedPCaDatasets_abida         17.894  2.455  21.525
curatedPCaDatasets_taylor        15.188  0.770  17.534
getPCa                           13.877  0.820  15.738
curatedPCaDatasets_tcga          13.904  0.781  15.997
curatedPCaDatasets_barbieri      13.178  0.882  15.087
curatedPCaDatasets_ren           12.786  0.609  15.044
curatedPCaDatasets_sun           11.574  0.606  13.265
curatedPCaDatasets_kim           11.514  0.606  13.282
curatedPCaDatasets_weiner        11.284  0.793  13.164
curatedPCaDatasets_kunderfranco  11.276  0.532  12.713
curatedPCaDatasets_wallace       10.873  0.659  12.563
curatedPCaDatasets_friedrich     10.909  0.565  12.369
curatedPCaDatasets_icgcca        10.531  0.604  12.138
curatedPCaDatasets_igc           10.534  0.545  11.944
curatedPCaDatasets_wang          10.286  0.758  12.074
curatedPCaDatasets_chandran      10.153  0.633  11.970
curatedPCaDatasets_true           9.248  0.492  10.551
curatedPCaDatasets_barwick        8.014  0.479   9.294
curatedPCaDatasets_baca           4.698  0.378   5.823
* 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.