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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:muleaData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings muleaData_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/muleaData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘muleaData/DESCRIPTION’ ... OK
* this is package ‘muleaData’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘muleaData’ 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 ... WARNING
Missing link or links in Rd file 'muleaData.Rd':
  ‘ExperimentHub’ ‘query’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  muleaData.Rd: ExperimentHub, query
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 ... WARNING
Functions or methods with usage in Rd file 'muleaData.Rd' but not in code:
  ‘query’

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'muleaData.Rd'
  ‘ExperimentHub::ExperimentHub()’ ‘muleaData’
Objects in \usage without \alias in Rd file 'muleaData.Rd':
  ‘query’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
muleaData 5.725   0.49   6.689
* 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: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/muleaData.Rcheck/00check.log’
for details.