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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CONFESS_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CONFESS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CONFESS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CONFESS’ version ‘1.34.0’
* 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 ‘CONFESS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CONFESS.Rcheck/00install.out’ for details.
* 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 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) Fluo_CV_modeling.Rd:34: Lost braces
    34 | Pseudotime(original) - median{Pseudotime(CV)} > pseudotime.cutoff. Default is 20.}
       |                              ^
checkRd: (-1) reestimate.pseudos.byCV.Rd:22: Lost braces
    22 | median{Pseudotime(CV)} > pseudotime.cutoff.}
       |       ^
checkRd: (-1) spotEstimator.Rd:56: Lost braces
    56 | min{(X-medX, Y-medY)} > cutoff and min{(X*-medX, Y*-medY)} > cutoff, the sample's location is set to (medX, medY); (2) if
       |    ^
checkRd: (-1) spotEstimator.Rd:56: Lost braces
    56 | min{(X-medX, Y-medY)} > cutoff and min{(X*-medX, Y*-medY)} > cutoff, the sample's location is set to (medX, medY); (2) if
       |                                       ^
checkRd: (-1) spotEstimator.Rd:57: Lost braces
    57 | min{(X*-medX, Y*-medY)} <= cutoff, the sample's location is set to (X*, Y*); (3) if min{(X-medX, Y-medY)} <= cutoff and
       |    ^
checkRd: (-1) spotEstimator.Rd:57: Lost braces
    57 | min{(X*-medX, Y*-medY)} <= cutoff, the sample's location is set to (X*, Y*); (3) if min{(X-medX, Y-medY)} <= cutoff and
       |                                                                                        ^
checkRd: (-1) spotEstimator.Rd:58: Lost braces
    58 | min{(X*-medX, Y*-medY)} > cutoff, the algorithm can either produce the solution of (1) or the solution of (2) depending
       |    ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'adjustFluo.Rd':
  ‘transform’

Documented arguments not in \usage in Rd file 'boxFluo.Rd':
  ‘transform’

Documented arguments not in \usage in Rd file 'doTransform.Rd':
  ‘transform’

Documented arguments not in \usage in Rd file 'failurecase.Rd':
  ‘origImg’

Documented arguments not in \usage in Rd file 'function.from.vector.Rd':
  ‘argument.vector’

Documented arguments not in \usage in Rd file 'invTransform.Rd':
  ‘transform’

Documented arguments not in \usage in Rd file 'isotone.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'joinAreas.Rd':
  ‘chaImgs’

Documented arguments not in \usage in Rd file 'orderFluo.Rd':
  ‘path.start’

Documented arguments not in \usage in Rd file 'readChaImg.Rd':
  ‘imgName’

Documented arguments not in \usage in Rd file 'summarizeAdjFluo.Rd':
  ‘transform’

Documented arguments not in \usage in Rd file 'which.min.diff.Rd':
  ‘vector’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Fluo_CV_prep    13.089  1.533  14.625
Fluo_adjustment  4.504  0.648   5.139
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CONFESS.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CONFESS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘CONFESS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
** testing if installed package keeps a record of temporary installation path
* DONE (CONFESS)