| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 | ||||
| Package 1804/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsamtools 2.22.0 (landing page) Bioconductor Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK |  | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: Rsamtools |
| Version: 2.22.0 |
| 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_2.22.0.tar.gz |
| StartedAt: 2024-11-09 11:54:56 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 11:59:35 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 279.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rsamtools.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### 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_2.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rsamtools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsamtools’ version ‘2.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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:
tabixfile.c:190:9: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rsamtools.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 2.7Mb
libs 1.4Mb
* 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 ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
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/4.4-arm64/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 13.311 0.128 13.439
* 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: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/Rsamtools.Rcheck/00check.log’
for details.
Rsamtools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsamtools
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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]
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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tabixfile.c -o tabixfile.o
tabixfile.c:190:9: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/bgzf.h:270:38: note: 'bgzf_is_bgzf' has been explicitly marked deprecated here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
^
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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -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/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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)
Rsamtools.Rcheck/tests/Rsamtools_unit_tests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, 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//Rtmpguau6B/file176c6252d293a/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//Rtmpguau6B/file176c66d0fa6c9'
[E::hts_idx_load3] Could not load local index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpguau6B/file176c66d0fa6c9' : No such file or directory
[E::idx_find_and_load] Could not retrieve index file for '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpguau6B/file176c61e8f0e0f'
[E::hts_idx_load3] Could not load local index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpguau6B/file176c61e8f0e0f' : 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 -- Sat Nov 9 11:59:31 2024
***********************************************
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
4.709 0.359 6.413
Rsamtools.Rcheck/Rsamtools-Ex.timings
| name | user | system | elapsed | |
| ApplyPileupsParam-class | 0.005 | 0.001 | 0.007 | |
| BamFile-class | 0.085 | 0.006 | 0.098 | |
| BamViews-class | 0.010 | 0.001 | 0.011 | |
| BcfFile-class | 0.056 | 0.005 | 0.063 | |
| FaFile-class | 0.013 | 0.000 | 0.012 | |
| PileupFiles-class | 0.002 | 0.000 | 0.002 | |
| Rsamtools-package | 0.003 | 0.000 | 0.003 | |
| ScanBamParam-class | 0.187 | 0.006 | 0.194 | |
| ScanBcfParam-class | 0 | 0 | 0 | |
| TabixFile-class | 0.009 | 0.000 | 0.010 | |
| applyPileups | 0 | 0 | 0 | |
| headerTabix | 0.000 | 0.001 | 0.001 | |
| indexTabix | 0.013 | 0.000 | 0.014 | |
| pileup | 13.311 | 0.128 | 13.439 | |
| quickBamFlagSummary | 0.008 | 0.001 | 0.009 | |
| readPileup | 0.019 | 0.001 | 0.021 | |
| scanBam | 0.157 | 0.014 | 0.171 | |
| scanBcf | 0.099 | 0.012 | 0.110 | |
| scanFa | 0.010 | 0.001 | 0.011 | |
| scanTabix | 0.013 | 0.001 | 0.014 | |
| seqnamesTabix | 0.001 | 0.000 | 0.001 | |
| testPairedEndBam | 0.004 | 0.000 | 0.005 | |
| zip | 0.013 | 0.001 | 0.014 | |