##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dada2.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* 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 'size_t' (aka 'unsigned long') [-Wformat]
  nwalign_vectorized.cpp:280:133: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/dada2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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
* 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.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘dada2’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c evaluate.cpp -o evaluate.o
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
  size_t len1 = 0, len2 = 0;
         ^
evaluate.cpp:327:20: warning: variable 'len2' 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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp:77:17: warning: variable 'nnw' set but not used [-Wunused-but-set-variable]
  static size_t nnw = 0;
                ^
nwalign_endsfree.cpp:221:17: warning: variable 'nnw' set but not used [-Wunused-but-set-variable]
  static size_t nnw = 0;
                ^
nwalign_endsfree.cpp:404:17: warning: variable 'nnw' set but not used [-Wunused-but-set-variable]
  static size_t nnw = 0;
                ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/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 '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:280:133: 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: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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/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 arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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 -L/Library/Frameworks/R.framework/Versions/4.5-arm64/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-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)