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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rifi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rifi_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rifi/DESCRIPTION’ ... OK
* this is package ‘rifi’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  R/.ipynb_checkpoints
  vignettes/.ipynb_checkpoints
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rifi’ can be installed ... WARNING
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
  Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
  Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
 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 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 ... WARNING
prepare_Rd: ./man/apply_Ttest_delay.Rd:55: unexpected '}'
prepare_Rd: ./man/predict_ps_itss.Rd:57: unexpected '}'
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00_pkg_src/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
rifi_wrapper       258.479 73.957 320.333
rifi_penalties     124.319 52.334 187.753
nls2_fit            97.616  5.143  69.995
rifi_fit            63.055  0.866  67.739
rifi_visualization  51.750  2.257  56.413
TI_fit              31.082  4.879  22.252
make_pen            23.214  8.852  33.843
rifi_fragmentation   7.984  1.789   9.872
rifi_stats           7.680  0.385   8.487
fold_change          7.639  0.348   8.093
rifi_preprocess      4.098  1.081   4.808
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/rifi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rifi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘rifi’ ...
** this is package ‘rifi’ version ‘1.12.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: next used in wrong context: no loop is visible 
** help
Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/apply_Ttest_delay.Rd:55: unexpected '}'
Warning: /Users/biocbuild/bbs-3.21-bioc/meat/rifi/man/predict_ps_itss.Rd:57: unexpected '}'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rifi)