Multiple platform build/check report for BioC 3.23 - CHECK results for Rsamtools on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4919
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4631
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 Rsamtools on kjohnson3

To the developers/maintainers of the Rsamtools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsamtools.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: Rsamtools

Version: 2.27.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsamtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsamtools_2.27.2.tar.gz

StartedAt: 2026-04-10 22:18:22 -0400 (Fri, 10 Apr 2026)

EndedAt: 2026-04-10 22:19:26 -0400 (Fri, 10 Apr 2026)

EllapsedTime: 64.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Rsamtools.Rcheck

Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsamtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsamtools_2.27.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsamtools.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-11 02:18:22 UTC
* using option ‘--no-vignettes’
* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsamtools’ version ‘2.27.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsamtools’ can be installed ... OK
* used C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... OK
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rsamtools/libs/Rsamtools.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
pileup 14.504  0.125  14.722
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsamtools.Rcheck/00check.log’
for details.

Installation output

Rsamtools.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsamtools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘Rsamtools’ ...
** this is package ‘Rsamtools’ version ‘2.27.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c PileupBuffer.cpp -o PileupBuffer.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c PosCacheColl.cpp -o PosCacheColl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ResultManager.cpp -o ResultManager.o
ResultManager.cpp:282:13: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  282 |         int i = 0;
      |             ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c as_bam.c -o as_bam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam.c -o bam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_data.c -o bam_data.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c bam_mate_iter.cpp -o bam_mate_iter.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_sort.c -o bam_sort.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bambuffer.c -o bambuffer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bamfile.c -o bamfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bcffile.c -o bcffile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bedidx.c -o bedidx.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c encode.c -o encode.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fafile.c -o fafile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c idxstats.c -o idxstats.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c io_sam.c -o io_sam.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pileup.cpp -o pileup.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pileupbam.c -o pileupbam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c samtools_patch.c -o samtools_patch.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c scan_bam_data.c -o scan_bam_data.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tabixfile.c -o tabixfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tagfilter.c -o tagfilter.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utilities.c -o utilities.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c zip_compression.c -o zip_compression.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-Rsamtools/00new/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsamtools)

Tests output

Rsamtools.Rcheck/tests/Rsamtools_unit_tests.Rout


R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('Rsamtools')

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'Biostrings'

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

    strsplit

[E::idx_find_and_load] Could not retrieve index file for ''
[E::hts_idx_load3] Could not load local index file '' : No such file or directory
[E::idx_find_and_load] Could not retrieve index file for '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpgswICS/file110f87883c3c4/index'
[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
[E::idx_find_and_load] Could not retrieve index file for '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpgswICS/file110f87f2ad978'
[E::hts_idx_load3] Could not load local index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpgswICS/file110f87f2ad978' : No such file or directory
[E::idx_find_and_load] Could not retrieve index file for '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpgswICS/file110f8562b9681'
[E::hts_idx_load3] Could not load local index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpgswICS/file110f8562b9681' : No such file or directory
[E::hts_idx_push] Chromosome blocks not continuous
[E::sam_index] Read 'B7_589:7:76:306:561' with ref_name='seq2', ref_length=1568, flags=83, pos=987 cannot be indexed
[E::hts_open_format] Failed to open file "http://httpbin.org/status/504" : Operation timed out


RUNIT TEST PROTOCOL -- Fri Apr 10 22:19:21 2026 
*********************************************** 
Number of test functions: 180 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rsamtools RUnit Tests - 180 test functions, 0 errors, 0 failures
Number of test functions: 180 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In applyPileups(PileupFiles(fl), identity) :
  'applyPileups' is deprecated.
Use 'pileup' instead.
See help("Deprecated")
2: In applyPileups(files, FUN, ..., param = plpParam(files)) :
  'applyPileups' is deprecated.
Use 'pileup' instead.
See help("Deprecated")
3: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
4: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
5: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
6: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
> 
> proc.time()
   user  system elapsed 
  5.331   0.696   7.233

Example timings

Rsamtools.Rcheck/Rsamtools-Ex.timings

name	user	system	elapsed
ApplyPileupsParam-class	0.009	0.002	0.012
BamFile-class	0.126	0.013	0.145
BamViews-class	0.012	0.002	0.014
BcfFile-class	0.082	0.005	0.088
FaFile-class	0.020	0.002	0.022
PileupFiles-class	0.003	0.000	0.004
Rsamtools-package	0.004	0.000	0.004
ScanBamParam-class	0.238	0.007	0.247
ScanBcfParam-class	0	0	0
TabixFile-class	0.014	0.001	0.015
applyPileups	0.000	0.001	0.000
headerTabix	0.001	0.000	0.001
indexTabix	0.018	0.003	0.021
pileup	14.504	0.125	14.722
quickBamFlagSummary	0.009	0.001	0.010
readPileup	0.021	0.001	0.024
scanBam	0.172	0.011	0.187
scanBcf	0.140	0.012	0.167
scanFa	0.013	0.001	0.015
scanTabix	0.013	0.002	0.015
seqnamesTabix	0.001	0.000	0.001
testPairedEndBam	0.004	0.001	0.005
zip	0.012	0.001	0.013