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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DECIPHER_3.2.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '3.2.0'
* 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 'DECIPHER' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable 'deltaGrulesRNA'
DesignSignatures: no visible binding for global variable 'deltaHrules'
FindGenes: no visible binding for global variable 'deltaHrulesRNA'
FindNonCoding: no visible binding for global variable 'deltaHrulesRNA'
LearnNonCoding: no visible binding for global variable 'deltaHrulesRNA'
PredictDBN: no visible binding for global variable 'deltaGrulesRNA'
Treeline: multiple local function definitions for '.NNI' with different
  formal arguments
Treeline: multiple local function definitions for '.minimize' with
  different formal arguments
Undefined global functions or variables:
  deltaGrulesRNA deltaHrules deltaHrulesRNA
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll':
  Found '_assert', possibly from 'assert' (C)
  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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AlignSeqs          211.43   8.33  219.94
TreeLine           177.92   7.28  185.52
LearnNonCoding     121.02   7.69  128.83
FindNonCoding       72.24  11.87   84.45
FindGenes           66.18   2.74   68.99
ExtractGenes        64.57   2.83   67.47
Genes-class         61.31   3.18   64.51
WriteGenes          59.60   3.67   63.50
BrowseSeqs          36.75   1.76   38.58
CorrectFrameshifts  20.89   0.92   21.87
StaggerAlignment    15.33   2.22   17.55
DetectRepeats       16.54   0.76   17.32
AlignTranslation    14.51   0.78   15.37
MapCharacters       11.61   0.54   12.14
IdTaxa              11.30   0.72   12.03
Taxa-class          10.80   0.88   11.68
Cophenetic          10.48   0.46   10.96
LearnTaxa            8.03   2.19   10.22
Array2Matrix         8.57   0.08    8.69
DesignArray          8.28   0.07    8.35
ScoreAlignment       6.53   0.61    7.14
Clusterize           6.25   0.60    6.84
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.