############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dada2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dada2_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/dada2.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'dada2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'dada2' version '1.32.0' * 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 whether package 'dada2' can be installed ... WARNING Found the following significant warnings: nwalign_vectorized.cpp:280:27: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:31: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:47: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:50: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:59: warning: format '%i' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:62: warning: format '%i' expects argument of type 'int', but argument 7 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:71: warning: format '%i' expects argument of type 'int', but argument 8 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] nwalign_vectorized.cpp:280:74: warning: format '%i' expects argument of type 'int', but argument 9 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] See 'F:/biocbuild/bbs-3.19-bioc/meat/dada2.Rcheck/00install.out' for details. * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.19-bioc/R/library/dada2/libs/x64/dada2.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PacBioErrfun 7.43 0.03 7.53 learnErrors 6.06 0.47 4.85 plotQualityProfile 2.98 0.09 19.71 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/dada2.Rcheck/00check.log' for details.