############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:atSNP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings atSNP_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/atSNP.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'atSNP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'atSNP' version '1.10.0' * 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 * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/atSNP/libs/i386/atSNP.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/atSNP/libs/x64/atSNP.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (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. 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMotifMatch 1.29 0.05 38.37 LoadFastaData 1.09 0.03 26.56 ComputePValues 0.92 0.03 12.81 dtMotifMatch 0.85 0.02 12.65 MatchSubsequence 0.77 0.04 13.37 ComputeMotifScore 0.78 0.01 13.74 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ComputePValues 0.99 0.03 30.12 dtMotifMatch 0.98 0.00 13.57 MatchSubsequence 0.88 0.00 12.96 ComputeMotifScore 0.78 0.05 13.33 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test.R' Running 'test_change.R' Running 'test_diff.R' Running 'test_is.R' OK ** running tests for arch 'x64' ... 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 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 'C:/Users/biocbuild/bbs-3.14-bioc/meat/atSNP.Rcheck/00check.log' for details.