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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DECIPHER_3.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... NOTE
  installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    data      7.5Mb
    extdata   2.5Mb
    libs      1.5Mb
* 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 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 ‘.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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
AlignSeqs          230.291  0.910 231.726
LearnNonCoding     118.863  2.039 121.158
TreeLine           110.429  0.498 111.211
FindNonCoding       75.101  0.562  75.817
ExtractGenes        56.324  0.260  56.730
FindGenes           54.671  0.359  58.388
Genes-class         52.801  0.128  53.043
WriteGenes          52.256  0.583  52.956
BrowseSeqs          29.351  0.084  29.495
CorrectFrameshifts  19.705  0.164  19.915
DetectRepeats       18.142  0.063  18.253
StaggerAlignment    15.811  0.144  15.995
AlignTranslation    15.646  0.063  15.744
Cophenetic          14.548  0.056  14.640
LearnTaxa           13.281  0.163  13.481
MapCharacters       11.557  0.121  11.715
Taxa-class          10.564  0.120  10.710
IdTaxa              10.329  0.059  10.414
ScoreAlignment       6.842  0.079   6.941
Clusterize           6.849  0.048   6.916
Array2Matrix         5.173  0.016   5.196
DesignArray          5.130  0.016   5.161
* 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-3.20-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.