############################################################################## ############################################################################## ### ### 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ version ‘1.13.0’ * 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 calculateDMN 102.608 0.428 117.695 runCCA 92.716 0.973 103.521 hierarchy-tree 51.694 1.440 60.362 agglomerate-methods 24.398 0.491 28.936 splitByRanks 20.748 0.276 24.119 estimateDiversity 19.286 1.252 22.025 getExperimentCrossAssociation 16.270 0.119 17.843 mergeSEs 16.062 0.300 17.380 makeTreeSEFromDADA2 13.353 0.514 14.886 getPrevalence 13.021 0.113 14.175 splitOn 10.685 0.093 12.239 summaries 9.179 0.144 10.644 importMetaPhlAn 8.817 0.055 10.026 calculateJSD 7.525 0.686 8.779 perSampleDominantTaxa 5.813 0.062 6.184 addDivergence 4.568 0.185 5.484 makePhyloseqFromTreeSE 4.473 0.131 5.071 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’