##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings tradeSeq_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/tradeSeq.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 ‘tradeSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tradeSeq’ version ‘1.12.0’
* 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 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
conditionTest           97.932  0.975 100.601
associationTest         56.771  1.072  59.733
plotSmoothers           41.688  0.169  41.860
fitGAM                  39.028  0.152  39.181
plotGeneCount           35.619  0.148  35.767
plot_evalutateK_results 21.539  0.080  21.621
evaluateK               20.993  0.252  21.246
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Monocle.Rmd’ using ‘UTF-8’... OK
  ‘fitGAM.Rmd’ using ‘UTF-8’... OK
  ‘multipleConditions.Rmd’ using ‘UTF-8’... OK
  ‘tradeSeq.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/tradeSeq.Rcheck/00check.log’
for details.