Benjamin Callahan
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/dada2 |
| git_branch: devel |
| git_last_commit: 3d68997 |
| git_last_commit_date: 2024-10-29 10:07:42 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:43 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 493/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dada2 1.35.0 (landing page) Benjamin Callahan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the dada2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dada2.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: dada2 |
| Version: 1.35.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dada2_1.35.0.tar.gz |
| StartedAt: 2025-01-10 19:54:34 -0500 (Fri, 10 Jan 2025) |
| EndedAt: 2025-01-10 19:59:10 -0500 (Fri, 10 Jan 2025) |
| EllapsedTime: 276.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: dada2.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dada2_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dada2.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.35.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dada2’ can be installed ... WARNING
Found the following significant warnings:
nwalign_vectorized.cpp:280:101: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
nwalign_vectorized.cpp:280:107: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
nwalign_vectorized.cpp:280:113: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
nwalign_vectorized.cpp:280:119: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
nwalign_vectorized.cpp:280:125: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
nwalign_vectorized.cpp:280:127: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
nwalign_vectorized.cpp:280:129: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
nwalign_vectorized.cpp:280:133: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/dada2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘ShortRead:::.set_omp_threads’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘C_isACGT’ ‘matchGenera’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
tax.check: warning in assignTaxonomy(sq.test, fn.tax, multi = TRUE):
partial argument match of 'multi' to 'multithread'
plotComplexity: no visible binding for global variable ‘complexity’
plotErrors: no visible binding for global variable ‘Qual’
plotErrors: no visible binding for global variable ‘Observed’
plotErrors: no visible binding for global variable ‘Input’
plotErrors: no visible binding for global variable ‘Estimated’
plotErrors: no visible binding for global variable ‘Nominal’
plotQualityProfile: no visible binding for global variable ‘Cycle’
plotQualityProfile: no visible binding for global variable ‘Score’
plotQualityProfile: no visible binding for global variable ‘Count’
plotQualityProfile: no visible binding for global variable ‘Mean’
plotQualityProfile: no visible binding for global variable ‘Q25’
plotQualityProfile: no visible binding for global variable ‘Q50’
plotQualityProfile: no visible binding for global variable ‘Q75’
plotQualityProfile: no visible binding for global variable ‘Cum’
tax.check: no visible binding for global variable ‘fn.spc’
Undefined global functions or variables:
Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
Qual Score complexity fn.spc
* checking Rd files ... NOTE
checkRd: (-1) dada-class.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:20: 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:
addSpecies.Rd: FastqStreamer
assignTaxonomy.Rd: setThreadOptions
dada.Rd: setThreadOptions
learnErrors.Rd: setThreadOptions
plotComplexity.Rd: geom_histogram, ggplot, ggsave
plotErrors.Rd: ggplot, ggsave
plotQualityProfile.Rd: ggplot, ggsave
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* 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
learnErrors 3.762 2.162 3.215
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 10 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/dada2.Rcheck/00check.log’
for details.
dada2.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dada2
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘dada2’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dada2.h:7:
./../inst/include/dada2_RcppExports.h:14:14: warning: unused function 'validateSignature' [-Wunused-function]
void validateSignature(const char* sig) {
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Rmain.cpp -o Rmain.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c chimera.cpp -o chimera.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster.cpp -o cluster.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c containers.cpp -o containers.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c error.cpp -o error.o
error.cpp:178:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c evaluate.cpp -o evaluate.o
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
size_t len1 = 0, len2 = 0;
^
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
size_t len1 = 0, len2 = 0;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c filter.cpp -o filter.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c kmers.cpp -o kmers.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c misc.cpp -o misc.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c nwalign_endsfree.cpp -o nwalign_endsfree.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp:280:101: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^~~~
%zu
nwalign_vectorized.cpp:280:107: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^~~~
%zu
nwalign_vectorized.cpp:280:113: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^~~~
%zu
nwalign_vectorized.cpp:280:119: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^~~~
%zu
nwalign_vectorized.cpp:280:125: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^
%zu
nwalign_vectorized.cpp:280:127: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^
%zu
nwalign_vectorized.cpp:280:129: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^~~
%lu
nwalign_vectorized.cpp:280:133: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
~~ ^~~~~~~~~~~~~~~~~~~
%lu
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
size_t start_col, end_col;
^
9 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pval.cpp -o pval.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp:145:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o dada2.so RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-dada2/00new/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (dada2)
dada2.Rcheck/dada2-Ex.timings
| name | user | system | elapsed | |
| PacBioErrfun | 4.062 | 0.309 | 4.421 | |
| addSpecies | 2.906 | 0.063 | 2.991 | |
| assignSpecies | 1.356 | 0.009 | 1.371 | |
| assignTaxonomy | 0.202 | 0.076 | 0.255 | |
| collapseNoMismatch | 0.467 | 0.025 | 0.496 | |
| dada | 2.990 | 0.080 | 3.085 | |
| derepFastq | 0.733 | 0.040 | 0.777 | |
| fastqFilter | 0.412 | 0.014 | 0.430 | |
| fastqPairedFilter | 0.670 | 0.030 | 0.706 | |
| filterAndTrim | 0.783 | 0.031 | 0.819 | |
| getDadaOpt | 0.000 | 0.001 | 0.001 | |
| getErrors | 0.781 | 0.027 | 0.815 | |
| getSequences | 0.253 | 0.021 | 0.276 | |
| getUniques | 0.254 | 0.018 | 0.276 | |
| inflateErr | 0.001 | 0.000 | 0.001 | |
| isBimera | 0.058 | 0.005 | 0.064 | |
| isBimeraDenovo | 2.173 | 0.043 | 2.227 | |
| isBimeraDenovoTable | 1.747 | 0.058 | 1.818 | |
| isPhiX | 0.151 | 0.008 | 0.160 | |
| isShiftDenovo | 0.788 | 0.015 | 0.809 | |
| learnErrors | 3.762 | 2.162 | 3.215 | |
| loessErrfun | 0.248 | 0.013 | 0.263 | |
| makeSequenceTable | 0.483 | 0.039 | 0.529 | |
| mergePairs | 2.504 | 0.155 | 2.675 | |
| mergeSequenceTables | 0.001 | 0.000 | 0.000 | |
| noqualErrfun | 0.499 | 0.012 | 0.512 | |
| nwalign | 0.001 | 0.001 | 0.000 | |
| nwhamming | 0.001 | 0.000 | 0.001 | |
| plotComplexity | 0.297 | 0.016 | 0.317 | |
| plotErrors | 2.148 | 0.054 | 2.220 | |
| plotQualityProfile | 3.640 | 0.338 | 3.992 | |
| rc | 0.017 | 0.003 | 0.020 | |
| removeBimeraDenovo | 2.335 | 0.187 | 2.549 | |
| removePrimers | 0.229 | 0.011 | 0.242 | |
| seqComplexity | 0.023 | 0.001 | 0.024 | |
| setDadaOpt | 0.001 | 0.001 | 0.001 | |
| uniquesToFasta | 0.076 | 0.011 | 0.088 | |