############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffBind_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DiffBind.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * 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 ‘DiffBind/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DiffBind’ version ‘3.14.0’ * 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 ‘DiffBind’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 2.0Mb extra 1.3Mb libs 1.1Mb * 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 whether startup messages can be suppressed ... 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) NEWS.Rd:106-115: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:431-438: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:440-446: Lost braces in \itemize; meant \describe ? checkRd: (-1) NEWS.Rd:450-456: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:96-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:99-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:102-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:126-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) DiffBind3.Rd:128-132: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:54-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:65-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:67-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:102-103: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:104-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:106-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:108-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:114-115: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:116-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:118-119: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:120-121: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.Rd:122-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.analyze.Rd:96-97: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.blacklist.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:32-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:55-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:62-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:66-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:87-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:92-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:217-219: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:221: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:223-226: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:228: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:233-234: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:236-237: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:253: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:255: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:257-258: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:267-268: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.normalize.Rd:270-271: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:90: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:91: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:92: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:93: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:105: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:110: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.peakset.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotHeatmap.Rd:148: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotHeatmap.Rd:149: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotHeatmap.Rd:150: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:58-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:64-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) dba.plotProfile.rd:70-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:53-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:57-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:81-82: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:85-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:89-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:102-109: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:112-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:116-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:123-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:130-133: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:136-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:142-145: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:148-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:153-155: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:158-159: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:162-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:166-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:170-171: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:174-175: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:178-180: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:183-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:188-190: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:193-195: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:198-200: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:203-204: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:207-208: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:211-212: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:215-216: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:219-220: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:223-224: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:227-228: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:231-232: Lost braces in \itemize; meant \describe ? checkRd: (-1) print.DBA.Rd:235-236: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DiffBind/libs/DiffBind.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed dba.contrast 44.870 0.788 46.045 dba.plotVenn 27.487 0.379 28.093 dba.normalize 23.300 0.413 23.889 dba.analyze 15.916 0.479 18.563 dba.plotMA 12.825 0.226 13.123 dba.plotHeatmap 8.344 0.135 8.342 dba.blacklist 7.955 0.103 8.171 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/DiffBind.Rcheck/00check.log’ for details.