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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings DECIPHER_3.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.5Mb
    libs      1.9Mb
* 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 loading without being on the library search path ... 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 ‘.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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
AlignSeqs          235.407  0.818 236.598
LearnNonCoding     141.438  1.325 142.973
MapCharacters      141.377  0.199 141.918
FindNonCoding      107.482  0.663 112.367
WriteGenes          63.686  0.184  63.999
ExtractGenes        62.680  0.219  63.006
Genes-class         60.800  0.171  61.079
FindGenes           60.864  0.096  61.066
BrowseSeqs          29.555  0.092  29.701
DetectRepeats       23.862  0.084  23.994
CorrectFrameshifts  20.850  0.040  20.933
LearnTaxa           17.460  0.212  17.705
StaggerAlignment    16.266  0.135  16.436
AlignTranslation    15.238  0.040  15.309
TreeLine            13.288  0.060  13.374
Taxa-class          12.962  0.056  13.046
IdTaxa              12.086  0.028  12.136
Clusterize           7.932  0.020   7.966
ScoreAlignment       6.909  0.068   6.996
Array2Matrix         5.348  0.060   5.418
DesignArray          5.254  0.068   5.329
TileSeqs             5.061  0.004   5.076
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.