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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.25.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.25.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ‘signatureSearch’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
  Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
  Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
Found the following additional notes/warnings:
  SystemRequirements specified C++11: support has been removed
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
  Obsolete C++11 standard request will be ignored
* checking installed package size ... INFO
  installed size is 85.3Mb
  sub-directories of 1Mb or more:
    R        81.0Mb
    data      2.0Mb
    extdata   1.9Mb
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘determine_refdb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GESSAttributeCatalog: no visible binding for global variable ‘Rank’
GESSAttributeCatalog: no visible global function definition for
  ‘median’
GESSAttributeCatalog: no visible binding for global variable ‘RowSums’
LINCSSigInfoGen: no visible binding for global variable ‘sedb’
connectivity_score_raw: no visible global function definition for
  ‘na.omit’
dsea_GSEA: no visible global function definition for
  ‘prepare_KEGG_drug’
dsea_hyperG: no visible global function definition for
  ‘prepare_KEGG_drug’
dtnetplot: no visible global function definition for ‘prepare_KEGG’
fgsea2 : <anonymous>: no visible global function definition for
  ‘na.omit’
gess_res_vis: no visible global function definition for ‘na.omit’
getAllSig : <anonymous>: no visible binding for global variable
  ‘pert_iname’
getAllSig: no visible binding for global variable ‘ENTREZID’
getAllSig: no visible binding for global variable ‘SYMBOL’
get_GO2TERM_table: no visible global function definition for
  ‘get_GOTERM’
tsea_dup_hyperG: no visible global function definition for ‘na.omit’
tsea_mGSEA: no visible global function definition for ‘na.omit’
tsea_mGSEA: no visible global function definition for ‘prepare_KEGG’
tsea_mGSEA: no visible global function definition for ‘gseKEGG2’
tsea_mabs: no visible global function definition for ‘na.omit’
tsea_mabs: no visible global function definition for ‘prepare_KEGG’
tsea_mabs: no visible global function definition for ‘mabsKEGG’
Undefined global functions or variables:
  ENTREZID Rank RowSums SYMBOL get_GOTERM gseKEGG2 mabsKEGG median
  na.omit pert_iname prepare_KEGG prepare_KEGG_drug sedb
Consider adding
  importFrom("stats", "median", "na.omit")
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 ... WARNING
  Warning: found non-ASCII string
  'medullary cystic<c2><a0>kidney<c2><a0>disease (MCKD) type 1' in object 'cell_info2'
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘signatureSearch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichMOA
> ### Title: MOA Category Enrichment with Hypergeometric Test
> ### Aliases: enrichMOA
> 
> ### ** Examples
> 
> emoa <- enrichMOA(gene = names(geneList)[seq(3)])
Error: object 'geneList' not found
Execution halted
* 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 ERROR, 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signatureSearch
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.25.1’
** using staged installation
** libs
specified C++11
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fastGSEA.cpp -o fastGSEA.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fgsea_init.c -o fgsea_init.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-signatureSearch/00new/signatureSearch/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** testing if installed package keeps a record of temporary installation path
* DONE (signatureSearch)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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.

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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(signatureSearch)
> # 
> # test_check("signatureSearch")
> 
> proc.time()
   user  system elapsed 
  0.103   0.038   0.136