Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-12 r89611) -- "Unsuffered Consequences"	920
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 teran2

To the developers/maintainers of the Rsamtools package:
- 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: 2.27.1

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:Rsamtools.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings Rsamtools_2.27.1.tar.gz

StartedAt: 2026-03-15 03:25:32 -0400 (Sun, 15 Mar 2026)

EndedAt: 2026-03-15 03:27:48 -0400 (Sun, 15 Mar 2026)

EllapsedTime: 136.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Rsamtools.Rcheck

Warnings: 2

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:Rsamtools.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings Rsamtools_2.27.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rsamtools.Rcheck’
* using R Under development (unstable) (2026-03-12 r89611)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* current time: 2026-03-15 07:25:33 UTC
* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsamtools’ version ‘2.27.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Bioconductor Package Maintainer <maintainer@bioconductor.org>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘Video’ ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Title field should be in title case. Current version is:
  ‘Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import’
In title case that is:
  ‘Binary Alignment (BAM), FASTA, Variant Call (BCF), and Tabix File Import’

The Description field should not start with the package name,
  'This package' or similar.
* 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 ... WARNING
Found the following significant warnings:
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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]
  bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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 ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rsamtools.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      6.7Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... 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 ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rsamtools/libs/Rsamtools.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
pileup 27.123  0.113  27.251
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rsamtools.Rcheck/00check.log’
for details.

Installation output

Rsamtools.Rcheck/00install.out

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL Rsamtools
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘Rsamtools’ ...
** this is package ‘Rsamtools’ version ‘2.27.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PosCacheColl.cpp -o PosCacheColl.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ResultManager.cpp -o ResultManager.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c as_bam.c -o as_bam.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bam.c -o bam.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bam_data.c -o bam_data.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from Template.h:9,
                 from BamIterator.h:10,
                 from BamRangeIterator.h:7,
                 from bam_mate_iter.cpp:1:
BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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]
   14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
  138 |         (void) bam_seek(bfile, pos, SEEK_SET);
      |                ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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]
   14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
   87 |         (void) bam_seek(bfile, 0, 0);
      |                ^~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bam_plbuf.c -o bam_plbuf.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bam_sort.c -o bam_sort.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bambuffer.c -o bambuffer.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bamfile.c -o bamfile.o
bamfile.c: In function ‘bamfile_isincomplete’:
bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  168 |             (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘_bam_tryindexload’,
    inlined from ‘_bamfile_open_r’ at bamfile.c:89:24,
    inlined from ‘bamfile_open’ at bamfile.c:127:17:
bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized [-Wmaybe-uninitialized]
   29 |         index = hts_idx_load2(file, indexname);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function ‘bamfile_open’:
bamfile.c:73:17: note: ‘cfile’ was declared here
   73 |     const char *cfile;
      |                 ^~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bcffile.c -o bcffile.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bedidx.c -o bedidx.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c encode.c -o encode.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fafile.c -o fafile.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c idxstats.c -o idxstats.o
In file included from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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]
   14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
   20 |     (void) bam_seek(fp, 0, 0);
      |            ^~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c io_sam.c -o io_sam.o
In file included from io_sam.c:3:
io_sam.c: In function ‘_scan_bam_all’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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]
   14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:302:12: note: in expansion of macro ‘bam_seek’
  302 |     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
      |            ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pileup.cpp -o pileup.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c pileupbam.c -o pileupbam.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c sam_opts.c -o sam_opts.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c sam_utils.c -o sam_utils.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c tabixfile.c -o tabixfile.o
tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  190 |     if (bgzf_is_bgzf(fn) != 1)
      |     ^~
In file included from tabixfile.c:3:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include/htslib/bgzf.h:270:9: note: declared here
  270 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
      |         ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c tagfilter.c -o tagfilter.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utilities.c -o utilities.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c zip_compression.c -o zip_compression.o
g++ -std=gnu++20 -shared -L/usr/local/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 /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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


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> 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 '/tmp/RtmpgJuAVU/file25e1765361c809/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 '/tmp/RtmpgJuAVU/file25e1761ce8a13b'
[E::hts_idx_load3] Could not load local index file '/tmp/RtmpgJuAVU/file25e1761ce8a13b' : No such file or directory
[E::idx_find_and_load] Could not retrieve index file for '/tmp/RtmpgJuAVU/file25e1766c365a'
[E::hts_idx_load3] Could not load local index file '/tmp/RtmpgJuAVU/file25e1766c365a' : 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" : Connection timed out


RUNIT TEST PROTOCOL -- Sun Mar 15 03:27:24 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 
 10.835   1.107  12.454

Example timings

Rsamtools.Rcheck/Rsamtools-Ex.timings

name	user	system	elapsed
ApplyPileupsParam-class	0.013	0.000	0.014
BamFile-class	0.239	0.019	0.294
BamViews-class	0.031	0.004	0.034
BcfFile-class	0.134	0.016	0.151
FaFile-class	0.040	0.000	0.041
PileupFiles-class	0.006	0.000	0.007
Rsamtools-package	0.007	0.000	0.008
ScanBamParam-class	0.617	0.045	0.662
ScanBcfParam-class	0	0	0
TabixFile-class	0.025	0.001	0.028
applyPileups	0.000	0.000	0.001
headerTabix	0.001	0.000	0.002
indexTabix	0.020	0.000	0.025
pileup	27.123	0.113	27.251
quickBamFlagSummary	0.020	0.001	0.021
readPileup	0.041	0.001	0.045
scanBam	0.310	0.019	0.329
scanBcf	0.189	0.000	0.190
scanFa	0.026	0.000	0.026
scanTabix	0.026	0.001	0.026
seqnamesTabix	0.002	0.000	0.002
testPairedEndBam	0.011	0.000	0.010
zip	0.017	0.000	0.018