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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:signifinder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings signifinder_1.9.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/signifinder.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.9.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘signifinder’ 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ADOSign.Rd: SummarizedExperiment-class
  APMSign.Rd: SummarizedExperiment-class
  ASCSign.Rd: SummarizedExperiment-class
  CD39CD8TcellSign.Rd: SummarizedExperiment-class
  CINSign.Rd: SummarizedExperiment-class
  CISSign.Rd: SummarizedExperiment-class
  COXISSign.Rd: SummarizedExperiment-class
  CombinedSign.Rd: SummarizedExperiment-class
  DNArepSign.Rd: SummarizedExperiment-class
  ECMSign.Rd: SummarizedExperiment-class
  EMTSign.Rd: SummarizedExperiment-class
  HRDSSign.Rd: SummarizedExperiment-class
  ICBResponseSign.Rd: SummarizedExperiment-class
  IFNSign.Rd: SummarizedExperiment-class
  IPRESSign.Rd: SummarizedExperiment-class
  IPSOVSign.Rd: SummarizedExperiment-class
  IPSSign.Rd: SummarizedExperiment-class
  IRGSign.Rd: SummarizedExperiment-class
  ISCSign.Rd: SummarizedExperiment-class
  LRRC15CAFSign.Rd: SummarizedExperiment-class
  MITFlowPTENnegSign.Rd: SummarizedExperiment-class
  MPSSign.Rd: SummarizedExperiment-class
  PassONSign.Rd: SummarizedExperiment-class
  SCSubtypeSign.Rd: SummarizedExperiment-class
  TGFBSign.Rd: SummarizedExperiment-class
  TLSSign.Rd: SummarizedExperiment-class
  TinflamSign.Rd: SummarizedExperiment-class
  VEGFSign.Rd: SummarizedExperiment-class
  autophagySign.Rd: SummarizedExperiment-class
  cellCycleSign.Rd: SummarizedExperiment-class
  chemokineSign.Rd: SummarizedExperiment-class
  consensusOVSign.Rd: SummarizedExperiment-class
  correlationSignPlot.Rd: SummarizedExperiment-class
  evaluationSignPlot.Rd: SummarizedExperiment-class
  expandedImmuneSign.Rd: SummarizedExperiment-class
  ferroptosisSign.Rd: SummarizedExperiment-class
  geneHeatmapSignPlot.Rd: SummarizedExperiment-class
  glycolysisSign.Rd: SummarizedExperiment-class
  heatmapSignPlot.Rd: SummarizedExperiment-class
  hypoxiaSign.Rd: SummarizedExperiment-class
  immuneCytSign.Rd: SummarizedExperiment-class
  immunoScoreSign.Rd: SummarizedExperiment-class
  interferonSign.Rd: SummarizedExperiment-class
  lipidMetabolismSign.Rd: SummarizedExperiment-class
  matrisomeSign.Rd: SummarizedExperiment-class
  metalSign.Rd: SummarizedExperiment-class
  mitoticIndexSign.Rd: SummarizedExperiment-class
  multipleSign.Rd: SummarizedExperiment-class
  oneSignPlot.Rd: SummarizedExperiment-class
  oxphosSign.Rd: SummarizedExperiment-class
  pyroptosisSign.Rd: SummarizedExperiment-class
  ridgelineSignPlot.Rd: SummarizedExperiment-class
  stateSign.Rd: SummarizedExperiment-class
  stemCellCD49fSign.Rd: SummarizedExperiment-class
  stressSign.Rd: SummarizedExperiment-class
  survivalSignPlot.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
multipleSign    146.120  0.814 146.939
consensusOVSign  73.038  0.300  73.353
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/signifinder.Rcheck/00check.log’
for details.