############################################################################## ############################################################################## ### ### Running command: ### ### /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 ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CONFESS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * 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 31.702 4.438 35.963 Fluo_adjustment 13.770 1.893 15.555 Fluo_modeling 12.253 0.899 13.152 * 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.