############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:atSNP.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings atSNP_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/atSNP.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'atSNP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'atSNP' version '1.21.0' * 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 whether package 'atSNP' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 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 Namespaces in Imports field not imported from: 'graphics' 'testthat' 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 ... NOTE ComputePValues: no visible binding for global variable 'motif' ComputePValues: no visible binding for global variable 'snpid' ComputePValues: no visible binding for global variable 'snpbase' ComputePValues: no visible binding for global variable 'pval_ref' ComputePValues: no visible binding for global variable 'pval_snp' ComputePValues: no visible binding for global variable 'pval_cond_ref' ComputePValues: no visible binding for global variable 'pval_cond_snp' ComputePValues: no visible binding for global variable 'pval_diff' ComputePValues: no visible binding for global variable 'pval_rank' LoadSNPData: no visible global function definition for 'is' LoadSNPData: no visible binding for global variable 'IUPAC_CODE_MAP' MatchSubsequence: no visible binding for global variable 'motif' MatchSubsequence: no visible binding for global variable 'snpid' MatchSubsequence: no visible binding for global variable 'snpbase' MatchSubsequence: no visible binding for global variable 'len_seq' MatchSubsequence: no visible binding for global variable 'ref_seq' MatchSubsequence : : no visible binding for global variable 'motif' checkMotifs: no visible global function definition for 'is' checkSNPids: no visible global function definition for 'is' dtMotifMatch: no visible binding for global variable 'ref_seq' dtMotifMatch: no visible binding for global variable 'len_seq' dtMotifMatch: no visible binding for global variable 'snp_ref_start' dtMotifMatch: no visible binding for global variable 'ref_start' dtMotifMatch: no visible binding for global variable 'snp_start' dtMotifMatch: no visible binding for global variable 'snp_ref_end' dtMotifMatch: no visible binding for global variable 'ref_end' dtMotifMatch: no visible binding for global variable 'snp_end' dtMotifMatch: no visible binding for global variable 'snp_ref_length' dtMotifMatch: no visible binding for global variable 'ref_aug_match_seq_forward' dtMotifMatch: no visible binding for global variable 'ref_aug_match_seq_reverse' dtMotifMatch: no visible binding for global variable 'snp_aug_match_seq_forward' dtMotifMatch: no visible binding for global variable 'snp_seq' dtMotifMatch: no visible binding for global variable 'snp_aug_match_seq_reverse' dtMotifMatch: no visible binding for global variable 'ref_strand' dtMotifMatch: no visible binding for global variable 'ref_location' dtMotifMatch: no visible binding for global variable 'snp_strand' dtMotifMatch: no visible binding for global variable 'snp_location' dtMotifMatch: no visible binding for global variable 'ref_extra_pwm_left' dtMotifMatch: no visible binding for global variable 'ref_extra_pwm_right' dtMotifMatch: no visible binding for global variable 'snp_extra_pwm_left' dtMotifMatch: no visible binding for global variable 'snp_extra_pwm_right' dtMotifMatch: no visible binding for global variable 'snpid' match_subseq_par: no visible binding for global variable 'snpid' match_subseq_par: no visible binding for global variable 'motif' match_subseq_par: no visible binding for global variable 'snpbase' match_subseq_par: no visible binding for global variable 'ref_strand' match_subseq_par: no visible binding for global variable 'ref_match_seq' match_subseq_par: no visible binding for global variable 'ref_seq' match_subseq_par: no visible binding for global variable 'ref_start' match_subseq_par: no visible binding for global variable 'ref_end' match_subseq_par: no visible binding for global variable 'ref_seq_rev' match_subseq_par: no visible binding for global variable 'len_seq' match_subseq_par: no visible binding for global variable 'snp_strand' match_subseq_par: no visible binding for global variable 'snp_match_seq' match_subseq_par: no visible binding for global variable 'snp_seq' match_subseq_par: no visible binding for global variable 'snp_start' match_subseq_par: no visible binding for global variable 'snp_end' match_subseq_par: no visible binding for global variable 'snp_seq_rev' match_subseq_par: no visible binding for global variable 'snp_seq_ref_match' match_subseq_par: no visible binding for global variable 'ref_seq_snp_match' match_subseq_par: no visible binding for global variable 'motif_len' match_subseq_par: no visible binding for global variable 'log_lik_ref' match_subseq_par: no visible binding for global variable 'log_lik_snp' match_subseq_par: no visible binding for global variable 'log_lik_ratio' match_subseq_par: no visible binding for global variable 'log_enhance_odds' match_subseq_par: no visible binding for global variable 'log_reduce_odds' match_subseq_par: no visible binding for global variable 'IUPAC' motif_score_par: no visible binding for global variable 'motif' motif_score_par: no visible binding for global variable 'snpbase' plotMotifMatch: no visible global function definition for 'is' results_motif_par: no visible binding for global variable 'p.value' Undefined global functions or variables: IUPAC IUPAC_CODE_MAP is len_seq log_enhance_odds log_lik_ratio log_lik_ref log_lik_snp log_reduce_odds motif motif_len p.value pval_cond_ref pval_cond_snp pval_diff pval_rank pval_ref pval_snp ref_aug_match_seq_forward ref_aug_match_seq_reverse ref_end ref_extra_pwm_left ref_extra_pwm_right ref_location ref_match_seq ref_seq ref_seq_rev ref_seq_snp_match ref_start ref_strand snp_aug_match_seq_forward snp_aug_match_seq_reverse snp_end snp_extra_pwm_left snp_extra_pwm_right snp_location snp_match_seq snp_ref_end snp_ref_length snp_ref_start snp_seq snp_seq_ref_match snp_seq_rev snp_start snp_strand snpbase snpid Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/atSNP/libs/x64/atSNP.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 ComputeMotifScore 2.34 0.01 17.22 dtMotifMatch 2.31 0.03 17.41 MatchSubsequence 2.23 0.02 18.26 ComputePValues 2.17 0.03 17.12 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test.R' Running 'test_change.R' Running 'test_diff.R' Running 'test_is.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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/atSNP.Rcheck/00check.log' for details.