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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:GenomicAlignments.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicAlignments_1.36.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GenomicAlignments.Rcheck'
* using R version 4.3.1 (2023-06-16 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 'GenomicAlignments/DESCRIPTION' ... OK
* this is package 'GenomicAlignments' version '1.36.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicAlignments' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomicRanges' 'Biostrings' 'Rsamtools'
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 ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since
  Cannot process chunk/lines:
    version 1.18.0
  Cannot process chunk/lines:
    No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since
  Cannot process chunk/lines:
    version 1.16.0
  Cannot process chunk/lines:
    The first version of GenomicAlignments was included in Bioconductor 2.14. 
  Cannot process chunk/lines:
    The package was created from existing code in IRanges, ShortRead, 
  Cannot process chunk/lines:
    Rsamtools and GenomicRanges. 
* 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
':::' calls which should be '::':
  'S4Vectors:::makeClassinfoRowForCompactPrinting'
  'S4Vectors:::makePrettyMatrixForCompactPrinting'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Rsamtools:::.BamViews_delegate' 'Rsamtools:::.findMateWithinGroups'
  'Rsamtools:::.load_bamcols_from_scanBam_res'
  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) GAlignmentPairs-class.Rd:90-94: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:102-133: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:138-143: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:144-160: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:161-172: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:173-179: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:184-188: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:189-193: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:194-203: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:204-210: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:211-216: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:217-222: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:223-232: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:240-244: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:252-257: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:258-264: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:272-298: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:299-328: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:329-336: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:337-340: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:348-359: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:148-154: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:162-165: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:166-171: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:172-179: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:184-190: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:191-195: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:196-202: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:203-213: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:214-221: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:222-227: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:228-232: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:233-241: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:242-248: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:249-254: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:255-260: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:261-270: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:278-292: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:293-335: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:336-344: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:351-357: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:365-369: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:375-381: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:388-400: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:67-70: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:78-81: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:82-85: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:86-90: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:95-99: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:100-105: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:106-112: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:113-118: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:119-123: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:124-129: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:130-134: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:135-139: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:140-146: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:147-152: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:153-158: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:170-187: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:188-206: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:207-215: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:216-222: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:223-228: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:236-240: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:245-250: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:256-262: \item in \describe must have non-empty label
checkRd: (5) GappedReads-class.Rd:40-44: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:133-137: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:138-155: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:156-182: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:183-185: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:186-192: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:200-204: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:213-227: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:228-235: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:236-245: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:246-261: \item in \describe must have non-empty label
checkRd: (5) summarizeOverlaps-methods.Rd:226-246: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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/GenomicAlignments/libs/x64/GenomicAlignments.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
junctions-methods          13.19   2.00   35.33
readGAlignments            12.11   0.53   20.37
sequenceLayer               8.30   1.10    9.83
summarizeOverlaps-methods   7.88   0.21   63.31
coordinate-mapping-methods  7.22   0.32    7.94
findSpliceOverlaps-methods  5.24   0.18    5.43
* 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: 1 WARNING, 5 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/GenomicAlignments.Rcheck/00check.log'
for details.