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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:curatedTBData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings curatedTBData_2.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedTBData.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 ‘curatedTBData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedTBData’ version ‘2.3.0’
* 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 ‘curatedTBData’ 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 ... NOTE
checkRd: (-1) DataSummary.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:47: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘Clinical_Information’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from Rd file 'DataSummary.Rd':
Variables in data frame 'DataSummary'
  Code: Age Control Country/Region DiagnosisMethod GEOAccession
        GeneralType HIVStatus LTBI Notes OD PTB Platform Tissue Total
  Docs: Age Control DiagnosisMethod GeneralType GeographicalRegion
        HIVStatus LTBI Notes OD PTB Platform Study Tissue Total

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
combine_objects 15.893  0.773  17.496
curatedTBData    9.983  0.540  11.297
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedTBData.Rcheck/00check.log’
for details.