############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings mia_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 109.839 0.044 110.775 runCCA 70.586 0.179 70.914 hierarchy-tree 34.939 0.236 35.259 estimateDiversity 16.403 0.103 16.544 agglomerate-methods 15.532 0.256 15.833 splitByRanks 11.727 0.028 11.782 makeTreeSEFromDADA2 10.193 0.122 10.341 mergeSEs 9.760 0.032 9.814 getExperimentCrossAssociation 9.135 0.048 9.206 calculateJSD 8.950 0.116 9.086 getPrevalence 7.419 0.044 7.482 splitOn 6.394 0.016 6.425 summaries 5.151 0.016 5.179 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck/00check.log’ for details.