############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ShortRead_1.63.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ShortRead/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ShortRead’ version ‘1.63.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ShortRead’ can be installed ... WARNING Found the following significant warnings: io.c:227:43: warning: format specifies type 'double' but the argument has type 'const char *' [-Wformat] io.c:659:23: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat] io.c:677:19: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: R 2.2Mb extdata 4.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * 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: ‘S4Vectors:::V_recycle’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .plotCycleBaseCall: no visible binding for global variable ‘Base’ flag,QAReadQuality: no visible binding for global variable ‘Score’ flag,QAReadQuality: no visible binding for global variable ‘Id’ flag,QAReadQuality: no visible binding for global variable ‘Density’ report,QAFrequentSequence: no visible binding for global variable ‘TopCount’ report,QAFrequentSequence: no visible binding for global variable ‘Id’ report,QANucleotideByCycle: no visible binding for global variable ‘Base’ report,QANucleotideUse: no visible binding for global variable ‘Nucleotide’ report,QAQualityUse: no visible binding for global variable ‘Count’ report,QAQualityUse: no visible binding for global variable ‘Id’ report,QAQualityUse: no visible binding for global variable ‘Quality’ report,QAReadQuality: no visible binding for global variable ‘Id’ report,QASequenceUse: no visible binding for global variable ‘Occurrences’ report,QASequenceUse: no visible binding for global variable ‘Id’ report,QASequenceUse: no visible binding for global variable ‘Reads’ Undefined global functions or variables: Base Count Density Id Nucleotide Occurrences Quality Reads Score TopCount * checking Rd files ... NOTE checkRd: (-1) deprecated.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) deprecated.Rd:23-24: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'ShortRead-package.Rd': ‘ShortReadBase-package’ * 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 line endings in shell scripts ... 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 ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ShortRead/libs/ShortRead.so’: Found ‘_sprintf’, possibly from ‘sprintf’ (C) 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 Snapshot-class 11.887 0.629 13.747 qa2 7.003 0.180 7.574 spViewPerFeature 4.844 0.614 5.962 readBaseQuality 4.462 0.298 5.178 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘ShortRead_unit_tests.R’ 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: 2 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck/00check.log’ for details.