Zheng Wei
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/Rbowtie2 |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8c4882b |
| git_last_commit_date: 2023-04-25 10:56:11 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:25 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1641/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie2 2.6.0 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the Rbowtie2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie2.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: Rbowtie2 |
| Version: 2.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbowtie2_2.6.0.tar.gz |
| StartedAt: 2023-10-16 05:50:50 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 05:51:57 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 67.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rbowtie2.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbowtie2_2.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rbowtie2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie2’ version ‘2.6.0’
* 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 ‘Rbowtie2’ can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* 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 ... OK
* 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 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bowtie2_samtools 8.273 0.765 10.902
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/Rbowtie2.Rcheck/00check.log’
for details.
Rbowtie2.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Rbowtie2’ ...
** using staged installation
** libs
mkdir -p ../inst
(cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
mv AdapterRemoval ../../inst/
(cd adapterremoval && (make clean_o -f Makefile))
rm -f *.o
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o bowtie2-build-s bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
-lpthread -lz
In file included from bt2_build.cpp:28:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_idx.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_io.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_util.cpp:26:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_party \
-o bowtie2-build-l bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
-lpthread -lz
In file included from bt2_build.cpp:28:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_idx.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_io.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_util.cpp:26:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o bowtie2-align-s bt2_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
-lpthread -lz
In file included from bt2_search.cpp:41:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_idx.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_io.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_util.cpp:26:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from aligner_seed.cpp:23:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:103:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from aligner_sw_driver.cpp:47:
In file included from ./aligner_sw_driver.h:84:
In file included from ./group_walk.h:86:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
aligner_sw_driver.cpp:1074:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
^
aligner_sw_driver.cpp:1769:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
^
3 warnings generated.
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:103:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_party \
-o bowtie2-align-l bt2_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
-lpthread -lz
In file included from bt2_search.cpp:41:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_idx.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_io.cpp:25:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from bt2_util.cpp:26:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from aligner_seed.cpp:23:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:103:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
In file included from aligner_sw_driver.cpp:47:
In file included from ./aligner_sw_driver.h:84:
In file included from ./group_walk.h:86:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
aligner_sw_driver.cpp:1074:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
^
aligner_sw_driver.cpp:1769:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
^
3 warnings generated.
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:103:
./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
1 warning generated.
(cd bowtie2-2.4.4 && (make move -f Makefile))
mv bowtie2-align-s ../../inst
mv bowtie2-build-s ../../inst
mv bowtie2-align-l ../../inst
mv bowtie2-build-l ../../inst
cp bowtie2 ../../inst
cp bowtie2-build ../../inst
(cd bowtie2-2.4.4 && (make clean_dSYM -f Makefile))
rm -rf *.dSYM
g++ -shared -fPIC -o Rbowtie2.so version_info.cpp
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rbowtie2/00new/Rbowtie2/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 (Rbowtie2)
Rbowtie2.Rcheck/Rbowtie2-Ex.timings
| name | user | system | elapsed | |
| adapterremoval_usage | 0.015 | 0.018 | 0.048 | |
| adapterremoval_version | 0.007 | 0.007 | 0.029 | |
| bowtie2-build | 1.118 | 0.607 | 1.521 | |
| bowtie2 | 1.003 | 0.367 | 1.070 | |
| bowtie2_build_usage | 0.138 | 0.051 | 0.206 | |
| bowtie2_samtools | 8.273 | 0.765 | 10.902 | |
| bowtie2_usage | 0.117 | 0.059 | 0.199 | |
| bowtie2_version | 0.113 | 0.053 | 0.190 | |
| identify_adapters | 0.025 | 0.020 | 0.049 | |
| remove_adapters | 0.045 | 0.034 | 0.087 | |