############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ShortRead_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ShortRead/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ShortRead’ version ‘1.60.0’ * 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: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] See ‘/home/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 7.8Mb 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 R 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 loading without being on the library search path ... 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 ... OK * 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 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 ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/ShortRead/libs/ShortRead.so’: Found ‘__sprintf_chk’, 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 5.981 0.236 6.228 * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Overview.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck/00check.log’ for details.