############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ShortRead_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ShortRead.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ShortRead/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ShortRead’ version ‘1.62.0’ * 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:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] See ‘/home/biocbuild/bbs-3.19-bioc/meat/ShortRead.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: R 2.1Mb 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 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 ... 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 ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 6.746 0.247 7.034 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘ShortRead_unit_tests.R’ ERROR Running the tests in ‘tests/ShortRead_unit_tests.R’ failed. Last 13 lines of output: FALSE FAILURE in test_readPrb_input: Error in checkIdentical(36L, unique(width(obj))) : FALSE Test files with failing tests test_readPrb.R test_readPrb_consistent test_readPrb_input Error in BiocGenerics:::testPackage("ShortRead") : unit tests failed for package ShortRead Execution halted * 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 ERROR, 2 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/ShortRead.Rcheck/00check.log’ for details.