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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tradeSeq_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/tradeSeq.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tradeSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tradeSeq’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘tradeSeq’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘igraph’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.earlyDETest: no visible binding for global variable ‘X1’
.earlyDETest: no visible binding for global variable ‘X2’
.findKnots: no visible binding for global variable ‘t1’
.findKnots: no visible binding for global variable ‘l1’
.plotGeneCount: no visible binding for global variable ‘dim1’
.plotGeneCount: no visible binding for global variable ‘dim2’
.plotSmoothers: no visible binding for global variable ‘time’
.plotSmoothers: no visible binding for global variable ‘gene_count’
.plotSmoothers: no visible binding for global variable ‘lineage’
.plotSmoothers_conditions: no visible binding for global variable
  ‘time’
.plotSmoothers_conditions: no visible binding for global variable
  ‘gene_count’
.plotSmoothers_conditions: no visible binding for global variable
  ‘lineage’
.plotSmoothers_conditions: no visible binding for global variable
  ‘pCol’
.plotSmoothers_sce: no visible binding for global variable ‘time’
.plotSmoothers_sce: no visible binding for global variable ‘gene_count’
.plotSmoothers_sce: no visible binding for global variable ‘lineage’
.plotSmoothers_sce: no visible binding for global variable ‘pCol’
Undefined global functions or variables:
  X1 X2 dim1 dim2 gene_count l1 lineage pCol t1 time
Consider adding
  importFrom("stats", "time")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) fitGAM.Rd:151-154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitGAM.Rd:155-156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitGAM.Rd:157-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitGAM.Rd:159-160: Lost braces in \itemize; meant \describe ?
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
conditionTest           147.274  6.774 154.946
plotSmoothers            58.190  5.457  63.892
associationTest          60.318  2.804  82.460
fitGAM                   54.341  4.393  59.172
plotGeneCount            45.651  6.058  51.939
evaluateK                22.929  0.455  23.656
plot_evalutateK_results  21.130  0.656  21.827
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/tradeSeq.Rcheck/00check.log’
for details.