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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signifinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signifinder_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/signifinder.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.12.0’
* 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 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       202.072  1.402 281.893
consensusOVSign    100.810  0.717 141.304
evaluationSignPlot   4.541  0.113   6.564
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/signifinder.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signifinder
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘signifinder’ ...
** this is package ‘signifinder’ version ‘1.12.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (signifinder)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(signifinder)

> 
> test_check("signifinder")
pyroptosisSignLi is using 100% of signature genes
ferroptosisSignLiang is using 100% of signature genes
lipidMetabolismSign is using 100% of signature genes
StemCellCD49fSign is using 100% of signature genes
glycolysisSignXu is using 100% of signature genes
autophagySignChenH is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
Loading required package: edgeR
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

autophagySignChenM is using 100% of OS signature genes
autophagySignChenM is using 60% of DFS signature genes
TinflamSign is using 100% of signature genes
interferonSign is using 100% of Interferon signature genes
EMTSignMiow is using 0% of epithelial signature genes
EMTSignMiow is using 100% of mesenchymal signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating  ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
EMTSignMiow is using 0% of epithelial signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating  ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
EMTSignMak is using 100% of epithelial signature genes
EMTSignMak is using 100% of mesenchymal signature genes
EMTSignMak is using 100% of mesenchymal signature genes
EMTSignCheng is using 100% of signature genes
EMTSignThompson is using 100% of epithelial signature genes
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
EMTSign is using 100% of cEMT signature genes
EMTSign is using 100% of pEMT signature genes
EMTSign is using 100% of pEMT signature genes
hipoxiaSign is using 100% of Hypoxia signature genes
ASCSign is using 100% of signature genes
ChemokineSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
PassONSign is using 100% of signature genes
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating  ssGSEA scores for 4 gene sets
i Calculating ranks
i Calculating rank weights
i Normalizing ssGSEA scores
v Calculations finished
CISSign is using 100% of up signature genes
CISSign is using 100% of down signature genes
CISSign is using 100% of down signature genes
HRDSSign is using 100% of signature genes
DNArepSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
IPRESSign is using 100% of signature genes
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating GSVA ranks
i kcdf='auto' (default)
i GSVA dense (classical) algorithm
i Row-wise ECDF estimation with Poisson kernels
i Calculating row ECDFs
i Calculating column ranks
i GSVA dense (classical) algorithm
i Calculating GSVA scores
v Calculations finished
ECMSign is using 0% of up signature genes
ECMSign is using 100% of down signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating  ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
ECMSign is using 0% of up signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating  ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
IPSOVSign is using 100% of signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
! Some gene sets have size one. Consider setting minSize > 1
i Calculating  ssGSEA scores for 15 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
! Some gene sets have size one. Consider setting minSize > 1
i Calculating  ssGSEA scores for 15 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
'select()' returned 1:1 mapping between keys and columns
stateSign is using 100% of MES2 signature genes
stateSign is using 100% of MES1 signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC1 signature genes
stateSign is using 100% of NPC2 signature genes
'select()' returned 1:1 mapping between keys and columns
stateSign is using 100% of MES1 signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC1 signature genes
stateSign is using 100% of NPC2 signature genes
stateSign is using 100% of Alveolar signature genes
stateSign is using 100% of Basal signature genes
stateSign is using 100% of Squamous signature genes
stateSign is using 100% of Glandular signature genes
stateSign is using 100% of Ciliated signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC signature genes
stateSign is using 100% of Basal signature genes
stateSign is using 100% of Squamous signature genes
stateSign is using 100% of Glandular signature genes
stateSign is using 100% of Ciliated signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC signature genes
TinflamSignThompson is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
cellCycleSign is using 100% of Cycle signature genes
EMTSignThompson is using 100% of epithelial signature genes
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
TinflamSignThompson is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
TinflamSignThompson is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
stateSign is using 100% of MITF signature genes
stateSign is using 100% of AXL signature genes
'select()' returned 1:1 mapping between keys and columns
stateSign is using 100% of AXL signature genes
'select()' returned 1:1 mapping between keys and columns
APMSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
APMSign is using 100% of signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating GSVA ranks
i kcdf='auto' (default)
i GSVA dense (classical) algorithm
i Row-wise ECDF estimation with Poisson kernels
i Calculating row ECDFs
i Calculating column ranks
i GSVA dense (classical) algorithm
i Calculating GSVA scores
v Calculations finished
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating GSVA ranks
i kcdf='auto' (default)
i GSVA dense (classical) algorithm
i Row-wise ECDF estimation with Poisson kernels
i Calculating row ECDFs
i Calculating column ranks
i GSVA dense (classical) algorithm
i Calculating GSVA scores
v Calculations finished
'select()' returned 1:1 mapping between keys and columns
MPSSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
IRGSign is using 100% of signature genes
TGFBSign is using 100% of signature genes
ADOSign is using 100% of signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating GSVA ranks
i kcdf='auto' (default)
i GSVA dense (classical) algorithm
i Row-wise ECDF estimation with Poisson kernels
i Calculating row ECDFs
i Calculating column ranks
i GSVA dense (classical) algorithm
i Calculating GSVA scores
v Calculations finished
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.1
i Searching for genes/features with constant values
i Calculating GSVA ranks
i kcdf='auto' (default)
i GSVA dense (classical) algorithm
i Row-wise ECDF estimation with Poisson kernels
i Calculating row ECDFs
i Calculating column ranks
i GSVA dense (classical) algorithm
i Calculating GSVA scores
v Calculations finished
MITFlowPTENnegSign is using 100% of signature genes
LRRC15CAFSign is using 100% of signature genes
SCSubtypeSign is using 0% of Basal signature genes
SCSubtypeSign is using 0% of Her2E signature genes
SCSubtypeSign is using 100% of LumA signature genes
SCSubtypeSign is using 0% of LumB signature genes
SCSubtypeSign is using 0% of Basal signature genes
SCSubtypeSign is using 0% of Her2E signature genes
SCSubtypeSign is using 0% of LumB signature genes
ICBResponseSign is using 0% of responder signature genes
ICBResponseSign is using 100% of nonresponder signature genes
ICBResponseSign is using 0% of responder signature genes
COXISSign is using 100% of signature genes
stressSign is using 100% of Stress signature genes
oxphosSign is using 100% of Oxphos signature genes
metalSign is using 100% of Metal signature genes
CD39CD8TcellSign is using 100% of signature genes
TLSSign is using 100% of signature genes
expandedImmuneSign is using 100% of signature genes
IFNSign is using 100% of signature genes
ImmuneCytSignRooney is using 100% of signature genes
mitoticIndexSign is using 100% of signature genes
matrisomeSign is using 100% of signature genes
immunoScoreSignRoh is using 100% of signature genes
CINSign is using 100% of signature genes
CINSign is using 36% of signature genes
CINSign is using 36% of signature genes
hypoxiaSign is using 100% of signature genes
cellCycleSignLundberg is using 100% of signature genes
cellCycleSignDavoli is using 100% of signature genes
VEGFSign is using 100% of signature genes
ImmuneCytSignDavoli is using 100% of signature genes
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 331 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 331 ]
> 
> proc.time()
   user  system elapsed 
702.873  20.185 996.072