############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mia’ 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 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) agglomerate-methods.Rd:73-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) agglomerate-methods.Rd:76-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) agglomerate-methods.Rd:78-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) agglomerate-methods.Rd:81-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) agglomerate-methods.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:94-96: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:97-100: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:101-103: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:104-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:149-151: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:153-162: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:164-165: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:167-176: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:178-183: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:185-192: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDiversity.Rd:194: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:99-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:103-112: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:114-126: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:128-137: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:139-147: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:149-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateDominance.Rd:160-175: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateEvenness.Rd:47-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateEvenness.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateEvenness.Rd:73-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateEvenness.Rd:75-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateEvenness.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateEvenness.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateRichness.Rd:87-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateRichness.Rd:106-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateRichness.Rd:119-126: Lost braces in \itemize; meant \describe ? checkRd: (-1) estimateRichness.Rd:128-131: Lost braces in \itemize; meant \describe ? checkRd: (-1) getExperimentCrossAssociation.Rd:66-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) getExperimentCrossAssociation.Rd:71-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) hierarchy-tree.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) hierarchy-tree.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) importHUMAnN.Rd:17-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) importHUMAnN.Rd:20-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) importHUMAnN.Rd:23-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) importMetaPhlAn.Rd:26-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) importMetaPhlAn.Rd:29-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) importMetaPhlAn.Rd:32-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) importMetaPhlAn.Rd:35-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) importMetaPhlAn.Rd:40-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) importQIIME2.Rd:47-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) importQIIME2.Rd:49-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) isContaminant.Rd:83-85: Lost braces in \itemize; meant \describe ? checkRd: (-1) isContaminant.Rd:86-87: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeTreeSEFromBiom.Rd:26-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) meltAssay.Rd:67-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) taxonomy-methods.Rd:101-102: Lost braces in \itemize; meant \describe ? checkRd: (-1) taxonomy-methods.Rd:116-117: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) taxonomy-methods.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) taxonomy-methods.Rd:119-122: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) transformAssay.Rd:118-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:154-155: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:157-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:160-161: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:163-164: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:166-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:169-170: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:172-176: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:178-182: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:184-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:187-188: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:190-191: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:193-194: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:196-197: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:199-200: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:202-203: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:205-207: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformAssay.Rd:209-210: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package ‘https’ in Rd xrefs * 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 ... NOTE Note: found 101 marked UTF-8 strings * 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 runCCA 59.354 0.773 60.689 calculateDMN 59.241 0.489 60.239 hierarchy-tree 26.299 1.713 28.302 estimateDiversity 12.868 1.741 14.748 agglomerate-methods 13.304 0.382 13.829 splitByRanks 10.064 0.252 10.406 mergeSEs 8.715 0.261 9.055 makeTreeSEFromDADA2 7.915 0.492 8.494 getExperimentCrossAssociation 7.782 0.124 8.003 calculateJSD 5.463 0.916 6.465 getPrevalence 6.140 0.140 6.351 splitOn 5.681 0.081 5.813 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck/00check.log’ for details.