############################################################################## ############################################################################## ### ### 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 4.4.1 (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 12.7.5 * 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 calculateDMN 102.991 0.634 133.171 runCCA 94.638 0.795 117.216 hierarchy-tree 52.409 1.336 70.415 agglomerate-methods 24.544 0.579 33.890 estimateDiversity 19.326 1.210 25.226 splitByRanks 20.117 0.175 24.592 getExperimentCrossAssociation 16.493 0.153 20.548 mergeSEs 15.832 0.259 19.792 makeTreeSEFromDADA2 13.427 0.488 17.207 getPrevalence 13.051 0.134 16.128 splitOn 10.586 0.128 13.227 importMetaPhlAn 8.892 0.223 11.212 summaries 8.782 0.073 10.655 calculateJSD 6.690 0.609 9.284 perSampleDominantTaxa 5.862 0.065 7.014 addDivergence 4.561 0.195 6.267 makePhyloseqFromTreeSE 4.364 0.098 5.625 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’