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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 489/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.28.0  (landing page)
Benjamin Callahan
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/dada2
git_branch: RELEASE_3_17
git_last_commit: 91f0208
git_last_commit_date: 2023-04-25 10:44:36 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

INSTALL results for dada2 on kjohnson2


To the developers/maintainers of the dada2 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: dada2
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dada2
StartedAt: 2023-10-15 16:38:57 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 16:41:53 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 175.3 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dada2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Rmain.cpp -o Rmain.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c chimera.cpp -o chimera.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cluster.cpp -o cluster.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c containers.cpp -o containers.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c filter.cpp -o filter.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c kmers.cpp -o kmers.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c misc.cpp -o misc.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c nwalign_endsfree.cpp -o nwalign_endsfree.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
  size_t start_col, end_col;
                    ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pval.cpp -o pval.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -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 arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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)