############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:DiffBind.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings DiffBind_3.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DiffBind.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘DiffBind/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DiffBind’ version ‘3.17.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... INFO installed size is 8.0Mb sub-directories of 1Mb or more: data 2.0Mb extra 1.3Mb libs 3.8Mb * 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: DiffBind-globals.Rd: SummarizedExperiment dba.Rd: SummarizedExperiment dba.analyze.Rd: DESeqDataSet dba.blacklist.Rd: GRanges, GRangesList, calcThreshold, GreyList dba.count.Rd: summarizeOverlaps dba.normalize.Rd: GRanges, SummarizedExperiment dba.peakset.Rd: GRanges dba.plotHeatmap.Rd: Dist, heatmap.2, GRanges dba.plotMA.Rd: GRanges dba.plotPCA.Rd: lattice, xyplot dba.plotProfile.rd: GRanges, GRangesList, mcols dba.plotVenn.Rd: vennPlot dba.report.Rd: SummarizedExperiment, GRanges print.DBA.Rd: summarizeOverlaps Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... INFO 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 ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/DiffBind/libs/DiffBind.so’: Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed dba.contrast 33.327 1.143 34.472 dba.plotVenn 22.489 0.470 22.959 dba.normalize 18.478 0.334 18.812 dba.analyze 11.301 0.765 12.069 dba.plotMA 11.054 0.290 11.348 dba.plotHeatmap 6.514 0.275 6.669 dba.blacklist 5.977 0.262 6.236 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/DiffBind.Rcheck/00check.log’ for details.