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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DECIPHER_2.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DECIPHER.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.26.0’
* 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
* checking installed package size ... NOTE
  installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.3Mb
    extdata   2.3Mb
    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 R 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
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 ‘deltaHrulesRNA’
TreeLine: multiple local function definitions for ‘.minimize’ with
  different formal arguments
Undefined global functions or variables:
  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
PredictDBN         106.584  0.232 106.818
MapCharacters       91.334  0.332  91.668
FindNonCoding       54.086  0.376  54.463
LearnNonCoding      49.823  3.986  54.364
BrowseSeqs          42.758  0.316  43.173
ExtractGenes        36.031  0.488  36.521
Genes-class         34.734  0.216  34.952
WriteGenes          34.156  0.096  34.252
FindGenes           31.414  0.184  31.599
AlignSeqs           21.619  0.367  21.987
CorrectFrameshifts  16.493  0.072  16.564
StaggerAlignment    11.408  0.084  11.493
AlignTranslation    11.211  0.152  11.365
Taxa-class          11.171  0.020  11.190
IdTaxa              10.603  0.040  10.643
DetectRepeats       10.047  0.111  10.159
TreeLine             7.601  0.052   7.652
LearnTaxa            6.805  0.828   7.633
Clusterize           5.218  0.056   5.274
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ArtOfAlignmentInR.Rnw’... OK
  ‘ClassifySequences.Rnw’... OK
  ‘ClusteringSequences.Rnw’... OK
  ‘DECIPHERing.Rnw’... OK
  ‘DesignMicroarray.Rnw’... OK
  ‘DesignPrimers.Rnw’... OK
  ‘DesignProbes.Rnw’... OK
  ‘DesignSignatures.Rnw’... OK
  ‘FindChimeras.Rnw’... OK
  ‘FindingGenes.Rnw’... OK
  ‘FindingNonCodingRNAs.Rnw’... OK
  ‘GrowingTrees.Rnw’... OK
  ‘RepeatRepeat.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.