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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsamtools.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Rsamtools_2.23.1.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Rsamtools.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '2.23.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rsamtools' can be installed ... WARNING
Found the following significant warnings:
  E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)' declared with attribute 'warn_unused_result' [-Wunused-result]
  E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include/bam_sort.c:3635:26: warning: unknown conversion type character 'z' in format [-Wformat=]
  E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include/bam_sort.c:3635:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include/bam_sort.c:3635:74: warning: unknown conversion type character 'z' in format [-Wformat=]
  E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include/bam_sort.c:3635:1: warning: too many arguments for format [-Wformat-extra-args]
  bamfile.c:168:20: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
  E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
  tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
See 'E:/biocbuild/bbs-3.21-bioc/meat/Rsamtools.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
  installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs     10.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::explodeIntBits' 'S4Vectors:::implodeIntBits'
  'S4Vectors:::makePowersOfTwo' 'S4Vectors:::quick_unlist'
  'S4Vectors:::selectSome'
  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 ... NOTE
checkRd: (-1) pileup.Rd:299-316: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BamFile-class.Rd: FilterRules, SimpleList, Seqinfo-class
  BamViews-class.Rd: DataFrame-class, GRanges-class
  BcfFile-class.Rd: SimpleList
  FaFile-class.Rd: GRanges-class, IntegerRangesList-class, SimpleList,
    DNAStringSet-class
  RsamtoolsFileList-class.Rd: SimpleList
  ScanBamParam-class.Rd: GRanges-class, IntegerRangesList-class
  TabixFile-class.Rd: SimpleList
  scanBam.Rd: FilterRules
  scanFa.Rd: GRanges-class, IntegerRangesList-class,
    DNAStringSet-class, RNAStringSet-class, AAStringSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/Rsamtools/libs/x64/Rsamtools.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'Rsamtools/libs/x64/Rsamtools.dll':
  Found non-API call to R: 'SET_TYPEOF'

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.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
pileup 40.72   0.39    42.2
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'Rsamtools_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.