############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:netboost.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netboost_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/netboost.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netboost/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netboost’ version ‘2.15.0’ * package encoding: UTF-8 * 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: .BBSoptions 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 ‘netboost’ can be installed ... WARNING Found the following significant warnings: boosting.cpp:415:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] boosting.cpp:415:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] HierarchicalClustering_with_unknown_edges.hpp:150:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] See ‘/home/biocbuild/bbs-3.21-bioc/meat/netboost.Rcheck/00install.out’ for details. * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * 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 ... NOTE BugReports field is not a suitable URL but appears to contain an email address not specified by mailto: nor contained in < > use the Contact field instead * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) cpp_filter_step.Rd:19: Lost braces 19 | Must be initialised before using @see{filter_base} | ^ * 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 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 ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * 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 cut_trees 14.441 0.235 15.486 nb_summary 14.220 0.092 15.389 nb_clust 13.765 0.080 15.099 nb_mcupgma 13.294 0.060 14.420 tree_search 13.275 0.048 14.459 nb_dist 12.971 0.060 13.773 nb_filter 9.057 0.044 10.063 * 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, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/netboost.Rcheck/00check.log’ for details.