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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 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘3.2.0’
* 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: ‘gcc (conda-forge gcc 14.2.0-1) 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          240.493  0.707 241.708
LearnNonCoding     137.261  1.477 138.935
TreeLine           113.911  0.279 114.431
FindNonCoding      109.611  1.290 111.581
ExtractGenes        64.748  0.358  62.427
Genes-class         64.280  0.160  63.565
FindGenes           62.598  0.111  60.021
WriteGenes          60.805  0.339  58.562
BrowseSeqs          29.878  0.091  30.016
CorrectFrameshifts  20.794  0.096  20.927
DetectRepeats       17.650  0.100  17.782
StaggerAlignment    16.794  0.116  16.942
LearnTaxa           16.673  0.136  16.833
AlignTranslation    15.317  0.116  15.459
Cophenetic          15.107  0.012  15.147
Taxa-class          12.120  0.092  12.233
MapCharacters       12.016  0.108  12.142
IdTaxa              11.293  0.012  11.324
Clusterize           7.206  0.064   7.289
ScoreAlignment       6.844  0.004   6.859
TileSeqs             5.485  0.004   5.500
Array2Matrix         5.373  0.052   5.431
DesignArray          5.357  0.040   5.405
* 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.