##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iSEEu_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/iSEEu.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘iSEEu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iSEEu’ version ‘1.17.0’
* 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 ‘iSEEu’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
Package in Depends field not imported from: ‘iSEEhex’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘iSEE:::.dataParamBoxOpen’ ‘iSEE:::.multiSelectHistory’
  ‘iSEE:::.noSelection’ ‘iSEE:::.organizationHeight’
  ‘iSEE:::.organizationWidth’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated.
  Warning in GeneSetTable(PanelId = 1L) : 'GeneSetTable' is deprecated.
  Warning in setPValuePattern(old) : 'setPValuePattern' is deprecated.
  Warning in .getIdentifierType() : '.getIdentifierType' is deprecated.
  Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getIdentifierType() : '.getIdentifierType' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
AggregatedDotPlot                 14.287  1.132  15.420
modeReducedDim                    11.905  0.436  12.339
DynamicMarkerTable-class           6.954  0.508   7.463
DynamicReducedDimensionPlot-class  6.874  0.468   7.343
modeGating                         5.484  0.432   5.917
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/iSEEu.Rcheck/00check.log’
for details.