############################################################################## ############################################################################## ### ### 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dada2.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘1.34.0’ * 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 ... 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-3.20-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 ... 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 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 ... NOTE 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 3.152 4.445 2.656 * 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-3.20-bioc/meat/dada2.Rcheck/00check.log’ for details.