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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_1.9.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/signifinder.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.9.1’
* 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 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
  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
  TGFBSign.Rd: SummarizedExperiment-class
  TLSSign.Rd: SummarizedExperiment-class
  TinflamSign.Rd: SummarizedExperiment-class
  VEGFSign.Rd: SummarizedExperiment-class
  autophagySign.Rd: SummarizedExperiment-class
  breastStateSign.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
  glioCellStateSign.Rd: SummarizedExperiment-class
  glycolysisSign.Rd: SummarizedExperiment-class
  heatmapSignPlot.Rd: SummarizedExperiment-class
  hypoxiaSign.Rd: SummarizedExperiment-class
  immuneCytSign.Rd: SummarizedExperiment-class
  immunoScoreSign.Rd: SummarizedExperiment-class
  lipidMetabolismSign.Rd: SummarizedExperiment-class
  matrisomeSign.Rd: SummarizedExperiment-class
  melStateSign.Rd: SummarizedExperiment-class
  mitoticIndexSign.Rd: SummarizedExperiment-class
  multipleSign.Rd: SummarizedExperiment-class
  oneSignPlot.Rd: SummarizedExperiment-class
  pyroptosisSign.Rd: SummarizedExperiment-class
  ridgelineSignPlot.Rd: SummarizedExperiment-class
  stemCellCD49fSign.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 ... ERROR
Running examples in ‘signifinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ADOSign
> ### Title: Adenosine Signaling Signature
> ### Aliases: ADOSign
> 
> ### ** Examples
> 
> data(ovse)
> ADOSign(dataset = ovse)
ADOSign is using 100% of signature genes
! 3 genes with constant values throughout the samples
! Genes with constant values are discarded
Error in `.mapGeneSetsToFeatures()`:
✖ No identifiers in the gene sets could be matched to the identifiers in
  the expression data.
Backtrace:
     ▆
  1. └─signifinder::ADOSign(dataset = ovse)
  2.   ├─base::as.vector(gsva(gsvaPar, verbose = FALSE))
  3.   ├─GSVA::gsva(gsvaPar, verbose = FALSE)
  4.   └─GSVA::gsva(gsvaPar, verbose = FALSE)
  5.     └─GSVA (local) .local(param, ...)
  6.       ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  7.       └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  8.         └─GSVA (local) .local(param, ...)
  9.           └─GSVA:::.filterAndMapGeneSets(...)
 10.             └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
 11.               └─cli::cli_abort(c(x = msg))
 12.                 └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    2.   ├─base::as.vector(gsva(gsvaPar, verbose = FALSE))
    3.   ├─GSVA::gsva(gsvaPar, verbose = FALSE)
    4.   └─GSVA::gsva(gsvaPar, verbose = FALSE)
    5.     └─GSVA (local) .local(param, ...)
    6.       ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
    7.       └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
    8.         └─GSVA (local) .local(param, ...)
    9.           └─GSVA:::.filterAndMapGeneSets(...)
   10.             └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
   11.               └─cli::cli_abort(c(x = msg))
   12.                 └─rlang::abort(...)
  
  [ FAIL 2 | WARN 9 | SKIP 0 | PASS 260 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-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’ ...
** 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
Warning in fun(libname, pkgname) :
  Package 'signifinder' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'signifinder' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (signifinder)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 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)

Warning message:
In fun(libname, pkgname) :
  Package 'signifinder' is deprecated and will be removed from
  Bioconductor version 3.22
> 
> test_check("signifinder")
'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

pyroptosisSignYe is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
ferroptosisSignYe 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
autophagySignChenM is using 100% of OS signature genes
autophagySignChenM is using 60% of DFS signature genes
TinflamSign is using 100% of signature genes
EMTSignMiow is using 0% of epithelial signature genes
EMTSignMiow is using 100% of mesenchymal signature genes
EMTSignMiow is using 0% of epithelial signature genes
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
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
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
! Input expression data has NA values, which will be propagated through calculations.
ECMSign is using 100% of up signature genes
ECMSign is using 0% of down signature genes
ECMSign is using 0% of down signature genes
IPSOVSign is using 100% of signature genes
! Duplicated gene IDs removed from gene set Antimicrobials
! Some gene sets have size one. Consider setting minSize > 1
! Duplicated gene IDs removed from gene set Antimicrobials
! Some gene sets have size one. Consider setting minSize > 1
'select()' returned 1:1 mapping between keys and columns
glioCellStateSign is using 100% of MES2 signature genes
glioCellStateSign is using 100% of MES1 signature genes
glioCellStateSign is using 100% of AC signature genes
glioCellStateSign is using 100% of OPC signature genes
glioCellStateSign is using 100% of NPC1 signature genes
glioCellStateSign is using 100% of NPC2 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
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
melStateSign is using 100% of MITF signature genes
melStateSign 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
'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
MITFlowPTENnegSign is using 100% of signature genes
LRRC15CAFSign is using 100% of signature genes
breastStateSign is using 100% of Basal signature genes
breastStateSign is using 100% of Her2E signature genes
breastStateSign is using 100% of LumA signature genes
breastStateSign is using 100% of LumB signature genes
breastStateSign is using 100% of Her2E signature genes
breastStateSign is using 100% of LumA signature genes
breastStateSign is using 100% of LumB signature genes
ICBResponseSign is using 100% of responder signature genes
ICBResponseSign is using 0% of nonresponder signature genes
ICBResponseSign is using 0% of nonresponder signature genes
COXISSign 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 2 | WARN 9 | SKIP 0 | PASS 260 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SignatureFunctions.R:193:3'): APMSign based on Wang's work ─────
Error in `.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))`: x No identifiers in the gene sets could be matched to the identifiers in the expression data.
Backtrace:
     ▆
  1. └─signifinder::APMSign(rmatrix) at test-SignatureFunctions.R:193:3
  2.   ├─GSVA::gsva(gsvaPar, verbose = FALSE)
  3.   └─GSVA::gsva(gsvaPar, verbose = FALSE)
  4.     └─GSVA (local) .local(param, ...)
  5.       ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  6.       └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  7.         └─GSVA (local) .local(param, ...)
  8.           └─GSVA:::.filterAndMapGeneSets(...)
  9.             └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
 10.               └─cli::cli_abort(c(x = msg))
 11.                 └─rlang::abort(...)
── Error ('test-SignatureFunctions.R:233:3'): ADOSign work ─────────────────────
Error in `.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))`: x No identifiers in the gene sets could be matched to the identifiers in the expression data.
Backtrace:
     ▆
  1. └─signifinder::ADOSign(rmatrix) at test-SignatureFunctions.R:233:3
  2.   ├─base::as.vector(gsva(gsvaPar, verbose = FALSE))
  3.   ├─GSVA::gsva(gsvaPar, verbose = FALSE)
  4.   └─GSVA::gsva(gsvaPar, verbose = FALSE)
  5.     └─GSVA (local) .local(param, ...)
  6.       ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  7.       └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  8.         └─GSVA (local) .local(param, ...)
  9.           └─GSVA:::.filterAndMapGeneSets(...)
 10.             └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
 11.               └─cli::cli_abort(c(x = msg))
 12.                 └─rlang::abort(...)

[ FAIL 2 | WARN 9 | SKIP 0 | PASS 260 ]
Error: Test failures
Execution halted