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This page was generated on 2023-03-28 11:05:47 -0400 (Tue, 28 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4301
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Biostrings on palomino3


To the developers/maintainers of the Biostrings package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biostrings.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 214/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.67.0  (landing page)
H. Pag├Ęs
Snapshot Date: 2023-03-27 14:00:21 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/Biostrings
git_branch: devel
git_last_commit: c94e8fb
git_last_commit_date: 2022-11-01 10:36:29 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Biostrings
Version: 2.67.0
Command: 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
StartedAt: 2023-03-27 23:44:25 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 23:54:03 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 578.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Biostrings.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 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/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 startup messages can be suppressed ... 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   235.17   1.73  236.94
matchPDict-inexact  60.85   0.58   61.43
findPalindromes     35.94   0.01   36.10
XStringSet-class    10.79   0.30   11.17
XStringSet-io        7.74   0.50   12.38
matchPattern         6.52   0.07    6.64
* 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/meat/Biostrings.Rcheck/00check.log'
for details.



Installation output

Biostrings.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Biostrings
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'Biostrings' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BAB_class.c -o BAB_class.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
  299 | static void BitMatrix_print(BitMatrix *bitmat)
      |             ^~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:184:27: warning: unused variable 'poffsets_order' [-Wunused-variable]
  184 |         IntAE *poffsets, *poffsets_order;
      |                           ^~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseList_utils.c -o SparseList_utils.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XStringSetList_class.c -o XStringSetList_class.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:124:17: warning: 'lkup_len' may be used uninitialized [-Wmaybe-uninitialized]
  124 |                 _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |                                 INTEGER(start)[i], lkup0, lkup_len);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
XStringSet_class.c:103:22: note: 'lkup_len' was declared here
  103 |         int ans_len, lkup_len, i;
      |                      ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XString_class.c -o XString_class.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:155:29: warning: 'sc' may be used uninitialized [-Wmaybe-uninitialized]
  155 |         INTEGER(ans_elt)[0] = score;
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~
align_needwunsQS.c:27:19: note: 'sc' was declared here
   27 |         int *sco, sc, n1, n2, i1, i2, j1, j2, al_buf_size;
      |                   ^~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:250:42: warning: 'indelWidthSubject' may be used uninitialized [-Wmaybe-uninitialized]
  250 |                                 jPattern += indelWidthSubject;
      |                                 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:78: note: 'indelWidthSubject' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                                                              ^~~~~~~~~~~~~~~~~
align_utils.c:231:63: warning: 'indelStartSubject' may be used uninitialized [-Wmaybe-uninitialized]
  231 |                         if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
      |                                                            ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:59: note: 'indelStartSubject' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                                           ^~~~~~~~~~~~~~~~~
align_utils.c:239:72: warning: 'indelWidthPattern' may be used uninitialized [-Wmaybe-uninitialized]
  239 |                                                 mappedStringPtr[index] = gapCodeValue;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
align_utils.c:221:40: note: 'indelWidthPattern' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                        ^~~~~~~~~~~~~~~~~
align_utils.c:232:78: warning: 'indelStartPattern' may be used uninitialized [-Wmaybe-uninitialized]
  232 |                                 if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
      |                                                                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:21: note: 'indelStartPattern' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                     ^~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_palindromes.c -o find_palindromes.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gtestsim.c -o gtestsim.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inject_code.c -o inject_code.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
  957 |   int x_width, y_width, x_length, *ans_mat, i, x_pos;
      |                                                ^~~~~
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
  956 |   SEXP ans, ans_dimnames;
      |             ^~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c lowlevel_matching.c -o lowlevel_matching.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_PWM.c -o match_PWM.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern.c -o match_pattern.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
    7 | static void test_match_pattern_indels(const char *p, const char *s,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict.c -o match_pdict.o
In function 'vcount_PDict3Parts_XStringSet',
    inlined from 'vmatch_PDict3Parts_XStringSet' at match_pdict.c:508:10:
match_pdict.c:419:33: warning: 'ans_col' may be used uninitialized [-Wmaybe-uninitialized]
  419 |                         ans_col += tb_length;
      |                         ~~~~~~~~^~~~~~~~~~~~
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:392:65: note: 'ans_col' was declared here
  392 |         int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
      |                                                                 ^~~~~~~
In function 'vcount_XStringSet_XStringSet',
    inlined from 'vmatch_XStringSet_XStringSet' at match_pdict.c:542:10:
match_pdict.c:470:41: warning: 'ans_elt' may be used uninitialized [-Wmaybe-uninitialized]
  470 |                                 ans_elt += P_length;
      |                                 ~~~~~~~~^~~~~~~~~~~
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:441:64: note: 'ans_elt' was declared here
  441 |         int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
      |                                                                ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1031 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1076:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1076 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
  602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
  139 | static void debug_node_counting_functions(int maxdepth)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:75:27: warning: 'twobit_sign2pos' may be used uninitialized [-Wmaybe-uninitialized]
   75 |         PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                           ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:19: note: 'twobit_sign2pos' was declared here
  110 |         SEXP ans, twobit_sign2pos;
      |                   ^~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:653:56: warning: unused variable 'ncol' [-Wunused-variable]
  653 |         int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
      |                                                        ^~~~
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:713:13: warning: unused variable 'nelt' [-Wunused-variable]
  713 |         int nelt, nkey0, nkey1, nkey2, i, key;
      |             ^~~~
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:820:51: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:820:34: warning: unused variable 'total_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:819:40: warning: unused variable 'NFC' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                        ^~~
match_pdict_utils.c:819:33: warning: unused variable 'nloci' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~~~
match_pdict_utils.c:819:27: warning: unused variable 'ndup' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                           ^~~~
match_pdict_utils.c: At top level:
match_pdict_utils.c:820:34: warning: 'total_NFC' defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:820:51: warning: 'subtotal_NFC' defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:261:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
  261 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_reporting.c -o match_reporting.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matchprobes.c -o matchprobes.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmatchPattern.c -o pmatchPattern.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_fasta_files.c -o read_fasta_files.o
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_files' at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_files':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_files' at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.length' may be used uninitialized [-Wmaybe-uninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_files':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_blocks' at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.ptr' is used uninitialized [-Wuninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_blocks':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_blocks' at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.length' is used uninitialized [-Wuninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_blocks':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function 'parse_FASTQ_file':
read_fastq_files.c:392:28: warning: 'dont_load' may be used uninitialized [-Wmaybe-uninitialized]
  392 |                         if (dont_load || loader->new_empty_seq_hook == NULL)
      |                            ^
read_fastq_files.c:309:26: note: 'dont_load' was declared here
  309 |             lineinrecno, dont_load;
      |                          ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c replaceAt.c -o replaceAt.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c replace_letter_at.c -o replace_letter_at.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c strutils.c -o strutils.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c translate.c -o translate.o
In function 'translate',
    inlined from 'DNAStringSet_translate' at translate.c:195:4:
translate.c:110:36: warning: 'if_ambig0' may be used uninitialized [-Wmaybe-uninitialized]
  110 |                                 if (if_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c: In function 'DNAStringSet_translate':
translate.c:136:36: note: 'if_ambig0' was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                                    ^~~~~~~~~
In function 'translate',
    inlined from 'DNAStringSet_translate' at translate.c:195:4:
translate.c:106:36: warning: 'if_non_ambig0' may be used uninitialized [-Wmaybe-uninitialized]
  106 |                                 if (if_non_ambig == TRANSLATE_TO_X)
      |                                    ^
translate.c: In function 'DNAStringSet_translate':
translate.c:136:21: note: 'if_non_ambig0' was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                     ^~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized]
  157 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c:150:16: note: 'twobit_sign' was declared here
  150 |         int i, twobit_sign;
      |                ^~~~~~~~~~~
utils.c: In function '_get_twobit_signature_at':
utils.c:164:19: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized]
  164 |         int i, j, twobit_sign;
      |                   ^~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xscat.c -o xscat.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h: In function 'XString_xscat':
F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:91:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized]
   91 | #define NEW_RAW(n)              Rf_allocVector(RAWSXP,n)
      |                                 ^~~~~~~~~~~~~~
xscat.c:18:20: note: 'ans_length' was declared here
   18 |         int nargs, ans_length, tag_offset, j;
      |                    ^~~~~~~~~~
xscat.c:52:23: warning: 'ans_classname' may be used uninitialized [-Wmaybe-uninitialized]
   52 |         PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                       ^~~~~~~~~~~~~~~~~
xscat.c:20:21: note: 'ans_classname' was declared here
   20 |         const char *ans_classname;
      |                     ^~~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h: In function 'XStringSet_xscat':
F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:85:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized]
   85 | #define NEW_INTEGER(n)          Rf_allocVector(INTSXP,n)
      |                                 ^~~~~~~~~~~~~~
xscat.c:66:39: note: 'ans_length' was declared here
   66 |         int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                       ^~~~~~~~~~
xscat.c:108:23: warning: 'ans_element_type' may be used uninitialized [-Wmaybe-uninitialized]
  108 |         PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                       ^~~~~~~~~~~~~~~~~
xscat.c:68:21: note: 'ans_element_type' was declared here
   68 |         const char *ans_element_type;
      |                     ^~~~~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-Biostrings/00new/Biostrings/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'twoWayAlphabetFrequencyByQuality' with signature '"QualityScaledXStringSet"': no definition for class "QualityScaledXStringSet"
Creating a new generic function for 'strsplit' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'pattern' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)

Tests output

Biostrings.Rcheck/tests/run_unitTests.Rout


R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> require("Biostrings") || stop("unable to load Biostrings package")
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> Biostrings:::.test()


RUNIT TEST PROTOCOL -- Mon Mar 27 23:53:44 2023 
*********************************************** 
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Biostrings RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In XStringSet("DNA", x, start = start, end = end, width = width,  :
  metadata columns on input DNAStringSet object were dropped
2: In XStringSet("DNA", x, start = start, end = end, width = width,  :
  metadata columns on input DNAStringSet object were dropped
3: In XStringSet("DNA", x, start = start, end = end, width = width,  :
  metadata columns on input DNAStringSet object were dropped
> 
> proc.time()
   user  system elapsed 
  10.14    1.21   11.50 

Example timings

Biostrings.Rcheck/Biostrings-Ex.timings

nameusersystemelapsed
AAString-class0.000.020.01
AMINO_ACID_CODE000
AlignedXStringSet-class0.050.000.04
DNAString-class000
GENETIC_CODE0.020.000.02
HNF4alpha0.000.010.01
IUPAC_CODE_MAP0.070.060.14
MIndex-class000
MaskedXString-class0.180.080.28
MultipleAlignment-class1.210.031.25
PDict-class3.570.113.72
PairwiseAlignments-class0.560.000.56
PairwiseAlignments-io2.330.062.40
QualityScaledXStringSet-class0.120.000.14
RNAString-class0.020.000.01
XString-class000
XStringQuality-class0.150.000.16
XStringSet-class10.79 0.3011.17
XStringSet-comparison2.630.082.70
XStringSet-io 7.74 0.5012.38
XStringSetList-class0.170.030.20
XStringViews-class0.110.000.11
align-utils0.010.030.05
chartr0.910.030.94
detail0.230.060.30
dinucleotideFrequencyTest0.000.020.01
findPalindromes35.94 0.0136.10
getSeq0.060.000.06
gregexpr2000
injectHardMask0.050.000.05
letter0.020.020.03
letterFrequency0.780.050.83
longestConsecutive000
lowlevel-matching0.280.010.29
maskMotif1.430.081.56
match-utils0.030.000.03
matchLRPatterns1.480.031.63
matchPDict-exact235.17 1.73236.94
matchPDict-inexact60.85 0.5861.43
matchPWM1.620.071.69
matchPattern6.520.076.64
matchProbePair1.830.051.88
matchprobes0.230.000.29
misc0.020.000.02
needwunsQS000
nucleotideFrequency0.430.060.70
padAndClip0.360.070.42
pairwiseAlignment0.690.060.75
phiX174Phage0.500.040.55
pid0.480.040.52
replaceAt1.970.072.04
replaceLetterAt0.370.080.45
reverseComplement0.960.030.99
seqinfo-methods0.570.020.60
stringDist2.910.032.94
substitution_matrices0.860.080.94
toComplex000
translate0.920.060.98
trimLRPatterns0.050.000.05
xscat0.850.020.87
yeastSEQCHR10.000.010.02