############################################################################## ############################################################################## ### ### 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 102.093 0.608 124.276 runCCA 94.411 0.803 110.054 hierarchy-tree 52.384 1.477 64.926 agglomerate-methods 23.542 0.410 29.271 splitByRanks 21.143 0.290 25.027 estimateDiversity 19.119 1.152 22.619 getExperimentCrossAssociation 16.344 0.143 19.049 mergeSEs 16.032 0.312 17.952 makeTreeSEFromDADA2 13.231 0.537 15.699 getPrevalence 13.265 0.162 15.807 splitOn 10.879 0.093 12.310 summaries 9.102 0.090 10.830 importMetaPhlAn 9.008 0.132 10.614 calculateJSD 6.469 0.650 7.962 perSampleDominantTaxa 5.884 0.080 6.767 addDivergence 4.694 0.373 6.577 makePhyloseqFromTreeSE 4.483 0.112 5.646 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’