############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CellNOptR_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CellNOptR.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CellNOptR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CellNOptR’ version ‘1.40.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'RBGL', 'graph', 'hash', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘CellNOptR’ can be installed ... OK * checking installed package size ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE build_sif_table_from_rule : rename_gates: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : rename_gates: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : simplify_gates: no visible global function definition for ‘filter’ build_sif_table_from_rule : simplify_gates: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : simplify_gates: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : interpret_sif_list: no visible global function definition for ‘setNames’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘num_or’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘new_node_out’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘new_node_in’ build_sif_table_from_rule : interpret_sif_list: no visible global function definition for ‘filter’ build_sif_table_from_rule : interpret_sif_list: no visible global function definition for ‘distinct’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘or_members’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘sign1’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘sign2’ crossvalidateBoolean: no visible global function definition for ‘error’ readBNET: no visible global function definition for ‘mutate’ readBNET: no visible binding for global variable ‘factors’ readBNET: no visible binding for global variable ‘i_and_gates’ readBNET: no visible binding for global variable ‘.’ Undefined global functions or variables: . distinct error factors filter i_and_gates mutate new_node_in new_node_out node_in node_out num_or or_members setNames sign1 sign2 Consider adding importFrom("stats", "filter", "setNames") to your NAMESPACE file. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... 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 ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_gaBinaryT1.R’ Running ‘test_gaBinaryT2.R’ Running ‘test_gaBinaryT3.R’ Running ‘test_import_rules.R’ Running ‘test_manySteadyStates.R’ Running ‘test_priorBitString.R’ Running ‘test_simulateTN.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/CellNOptR.Rcheck/00check.log’ for details.