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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Biostrings.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Biostrings_2.67.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Biostrings.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.67.0'
* 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 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Biostrings.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'IRanges:::.showAtomicList'
  'IRanges:::from_Vector_to_CompressedList'
  'IRanges:::new_CompressedList_from_list' 'IRanges:::new_Views'
  'IRanges:::regroupBySupergroup' 'IRanges:::show_IntegerRangesList'
  'IRanges:::unlist_as_integer' 'S4Vectors:::anyMissingOrOutside'
  'XVector:::close_filexp'
  'XVector:::extract_character_from_XRaw_by_positions'
  'XVector:::extract_character_from_XRaw_by_ranges'
  'XVector:::new_XVectorList_from_list_of_XVector'
  'XVector:::open_output_file'
  See the note in ?`:::` about the use of this operator.
* 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 non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:126-129: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:138-141: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:147-151: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:152-156: \item in \describe must have non-empty label
checkRd: (5) DNAString-class.Rd:57-61: \item in \describe must have non-empty label
checkRd: (5) DNAString-class.Rd:69-75: \item in \describe must have non-empty label
checkRd: (5) InDel-class.Rd:32-35: \item in \describe must have non-empty label
checkRd: (5) InDel-class.Rd:36-39: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (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 label
checkRd: (5) MaskedXString-class.Rd:146-152: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:160-164: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:165-168: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:169-172: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:180-185: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:193-197: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:198-203: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:157-161: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:162-167: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:168-178: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:179-189: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:190-200: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:201-216: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:217-220: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:221-224: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:225-228: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:229-232: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:233-236: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:237-240: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:245-249: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:250-253: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:261-267: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:268-274: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:275-282: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:290-298: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:299-304: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:305-312: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:313-320: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:321-337: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:245-249: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:250-253: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:254-257: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:258-261: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:262-269: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:270-273: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:282-285: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:294-297: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:298-301: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:154-160: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:161-165: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:166-169: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:177-180: \item in \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) QualityScaledXStringSet-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:124-129: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:143-146: \item in \describe must have non-empty label
checkRd: (5) RNAString-class.Rd:55-59: \item in \describe must have non-empty label
checkRd: (5) RNAString-class.Rd:67-73: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:94-98: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:106-111: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:112-115: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:123-126: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:127-130: \item in \describe must have non-empty label
checkRd: (5) 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
checkRd: (5) XStringSet-class.Rd:239-242: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:251-254: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:255-258: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:259-262: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:263-266: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:275-280: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:281-286: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:287-290: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:291-298: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:299-302: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:303-311: \item in \describe must have non-empty label
checkRd: (5) 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/libs/x64/Biostrings.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
matchPDict-exact   213.86   1.62  215.48
findPalindromes     33.55   0.03   33.61
matchPDict-inexact  31.83   0.40   32.23
XStringSet-io        8.20   0.28    8.65
XStringSet-class     7.25   0.35    7.77
matchPattern         6.66   0.08    6.73
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Biostrings.Rcheck/00check.log'
for details.