############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Biostrings_2.68.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘Biostrings/DESCRIPTION’ ... OK * this is package ‘Biostrings’ version ‘2.68.1’ * 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 ‘Biostrings’ can be installed ... WARNING Found the following significant warnings: read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ is used uninitialized [-Wuninitialized] read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ is used uninitialized [-Wuninitialized] See ‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 13.7Mb sub-directories of 1Mb or more: R 1.3Mb extdata 11.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 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 ... WARNING checkRd: (5) AAString-class.Rd:74-78: \item in \describe must have non-empty label checkRd: (5) AAString-class.Rd:86-92: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:87-90: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:91-96: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:97-99: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:100-103: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:104-107: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:108-111: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:112-116: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:117-121: \item in \describe must have non-empty label checkRd: (5) AlignedXStringSet-class.Rd:122-125: \item in \describe must have 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(5) MIndex-class.Rd:53-56: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:57-61: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:62-66: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:67-71: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:79-83: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:91-99: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:110-115: \item in \describe must have non-empty label checkRd: (5) MIndex-class.Rd:116-119: \item in \describe must have non-empty label checkRd: (5) MaskedXString-class.Rd:113-116: \item in \describe must have non-empty label checkRd: (5) MaskedXString-class.Rd:117-122: \item in \describe must have non-empty label checkRd: (5) MaskedXString-class.Rd:123-140: \item in \describe must have non-empty label checkRd: (5) MaskedXString-class.Rd:141-145: \item in \describe must have non-empty 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\describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:181-187: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:188-193: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:202-210: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:211-214: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:215-218: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:219-222: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:230-234: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:235-238: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:239-243: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:244-250: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:258-262: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:263-268: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:269-274: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:275-279: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:280-283: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:284-289: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:295-299: \item in \describe must have non-empty label checkRd: (5) PairwiseAlignments-class.Rd:300-304: \item in \describe must have non-empty label checkRd: (5) QualityScaledXStringSet-class.Rd:111-114: \item in \describe must have non-empty label checkRd: (5) QualityScaledXStringSet-class.Rd:115-119: \item in \describe must have non-empty label checkRd: (5) 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XString-class.Rd:138-148: \item in \describe must have non-empty label checkRd: (5) XString-class.Rd:156-169: \item in \describe must have non-empty label checkRd: (5) XString-class.Rd:170-173: \item in \describe must have non-empty label checkRd: (5) XStringPartialMatches-class.Rd:32-35: \item in \describe must have non-empty label checkRd: (5) XStringPartialMatches-class.Rd:36-39: \item in \describe must have non-empty label checkRd: (5) XStringPartialMatches-class.Rd:49-54: \item in \describe must have non-empty label checkRd: (-1) XStringQuality-class.Rd:86: Escaped LaTeX specials: \# checkRd: (5) XStringQuality-class.Rd:106-109: \item in \describe must have non-empty label checkRd: (5) XStringQuality-class.Rd:111-115: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:116-118: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:119-121: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:122-124: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:135-138: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:139-145: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:146-155: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:156-162: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:163-166: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:176-193: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:194-204: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:205-215: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:216-221: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:231-234: \item in \describe must have non-empty label checkRd: (5) XStringSet-class.Rd:235-238: \item in \describe must have non-empty label 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XStringSet-comparison.Rd:55-65: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:66-72: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:80-85: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:86-90: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:91-94: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:95-98: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:106-109: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:110-113: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:122-126: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:127-131: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:141-143: \item in \describe must have non-empty label checkRd: (5) XStringSet-comparison.Rd:144-146: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:73-77: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:87-93: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:103-117: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:118-121: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:122-131: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:136-143: \item in \describe must have non-empty label checkRd: (5) XStringViews-class.Rd:144-147: \item in \describe must have non-empty label checkRd: (5) injectHardMask.Rd:58-61: \item in \describe must have non-empty label checkRd: (5) injectHardMask.Rd:62-70: \item in \describe must have non-empty label checkRd: (5) injectHardMask.Rd:71-74: \item in \describe must have non-empty label checkRd: (-1) matchLRPatterns.Rd:65: Escaped LaTeX specials: \_ \_ checkRd: (-1) matchProbePair.Rd:53: Escaped LaTeX specials: \_ \_ checkRd: (-1) matchProbePair.Rd:54: Escaped LaTeX specials: \_ \_ checkRd: (-1) matchProbePair.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) matchProbePair.Rd:56: Escaped LaTeX specials: \_ \_ checkRd: (-1) phiX174Phage.Rd:18: Escaped LaTeX specials: \_ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘strsplit’ ‘twoWayAlphabetFrequency’ Undocumented S4 methods: generic 'match' and siglist 'Vector,XStringSet' generic 'match' and siglist 'XStringSet,Vector' generic 'match' and siglist 'XStringSet,vector' generic 'match' and siglist 'vector,XStringSet' generic 'parallel_slot_names' and siglist 'ByPos_MIndex' generic 'parallel_slot_names' and siglist 'MIndex' generic 'pcompare' and siglist 'Vector,XStringSet' generic 'pcompare' and siglist 'XStringSet,Vector' generic 'pcompare' and siglist 'XStringSet,vector' generic 'pcompare' and siglist 'vector,XStringSet' generic 'relistToClass' and siglist 'XString' generic 'strsplit' and siglist 'XStringSet' generic 'twoWayAlphabetFrequency' and siglist 'XString,XString' generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet' generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString' generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet' generic 'unstrsplit' and siglist 'XStringSet' generic 'unstrsplit' and siglist 'XStringSetList' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed matchPDict-exact 277.327 1.732 279.063 matchPDict-inexact 50.470 0.316 50.785 findPalindromes 38.571 0.088 38.665 XStringSet-class 9.564 0.316 9.882 XStringSet-io 7.693 0.271 7.967 matchPattern 5.382 0.212 5.594 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Biostrings2Classes.Rnw’ using ‘UTF-8’... OK ‘BiostringsQuickOverview.Rnw’ using ‘UTF-8’... OK ‘MultipleAlignments.Rnw’ using ‘UTF-8’... OK ‘PairwiseAlignments.Rnw’ using ‘UTF-8’... OK ‘matchprobes.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck/00check.log’ for details.