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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:atSNP.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings atSNP_1.23.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/atSNP.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 '1.23.0'
* 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) 13.3.0'
* 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 : <anonymous>: 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 'E:/biocbuild/bbs-3.21-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
dtMotifMatch      2.37   0.00   20.69
ComputePValues    2.23   0.03   21.25
MatchSubsequence  2.20   0.01   20.58
ComputeMotifScore 2.03   0.05   19.94
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/atSNP.Rcheck/00check.log'
for details.