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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signeR_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/signeR.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signeR’ version ‘2.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 49 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 ‘signeR’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* 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 ... NOTE
covariate: no visible binding for global variable ‘.’
cox_as_data_frame2: no visible binding for global variable ‘term’
cox_as_data_frame2: no visible binding for global variable ‘estimate’
cox_as_data_frame2: no visible binding for global variable ‘conf.low’
cox_as_data_frame2: no visible binding for global variable ‘conf.high’
cox_as_data_frame2: no visible binding for global variable ‘p.value’
explorepage: no visible binding for global variable ‘.’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Variant_Type’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Reference_Allele’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Tumor_Seq_Allele2’
genCountMatrixFromMAF: no visible binding for global variable
  ‘Tumor_Seq_Allele1’
signeRFlow : server : loadSig: no visible binding for global variable
  ‘sig’
signeRFlow : server : loadSig: no visible binding for global variable
  ‘sig_test’
tcgaexplorer : get_similarities_tcga: no visible binding for global
  variable ‘project’
tcgaexplorer: no visible binding for global variable ‘.’
DiffExp,SignExp-character: no visible binding for global variable ‘fc’
ExposureBarplot,SignExp: no visible binding for global variable
  ‘Samples’
ExposureBarplot,SignExp: no visible binding for global variable
  ‘Signatures’
ExposureBoxplot,SignExp: no visible binding for global variable
  ‘Signatures’
ExposureBoxplot,SignExp: no visible binding for global variable
  ‘Samples’
ExposureClassify,ANY-character: no visible binding for global variable
  ‘Col’
ExposureClassify,ANY-character: no visible binding for global variable
  ‘Frequency’
ExposureClassify,ANY-character: no visible binding for global variable
  ‘Row’
ExposureClassifyCV,ANY-character: no visible binding for global
  variable ‘Col’
ExposureClassifyCV,ANY-character: no visible binding for global
  variable ‘Frequency’
ExposureClassifyCV,ANY-character: no visible binding for global
  variable ‘Row’
ExposureCorrelation,SignExp-numeric: no visible binding for global
  variable ‘Feature’
ExposureCorrelation,SignExp-numeric: no visible binding for global
  variable ‘exposure’
ExposureCorrelation,matrix-numeric: no visible binding for global
  variable ‘Feature’
ExposureCorrelation,matrix-numeric: no visible binding for global
  variable ‘exposure’
Undefined global functions or variables:
  . Col Feature Frequency Reference_Allele Row Samples Signatures
  Tumor_Seq_Allele1 Tumor_Seq_Allele2 Variant_Type conf.high conf.low
  estimate exposure fc p.value project sig sig_test term
* checking Rd files ... NOTE
prepare_Rd: cosmic_data.Rd:91-93: Dropping empty section \details
prepare_Rd: cosmic_data.Rd:98-100: Dropping empty section \references
prepare_Rd: cosmic_data.Rd:101-102: Dropping empty section \examples
prepare_Rd: tcga_similarities.Rd:96-98: Dropping empty section \details
prepare_Rd: tcga_similarities.Rd:99-101: Dropping empty section \source
prepare_Rd: tcga_similarities.Rd:102-104: Dropping empty section \references
prepare_Rd: tcga_similarities.Rd:105-106: Dropping empty section \examples
prepare_Rd: tcga_tumors.Rd:18-20: Dropping empty section \details
prepare_Rd: tcga_tumors.Rd:21-23: Dropping empty section \source
prepare_Rd: tcga_tumors.Rd:24-26: Dropping empty section \references
prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
ExposureClassifyCV      80.326  0.374  81.777
ExposureClassify        21.507  0.191  21.867
ExposureSurvModel       21.480  0.131  22.119
ExposureFuzzyClustering 14.689  0.098  14.910
Diffexp                  6.644  0.388   7.106
genMatrix                5.651  0.227   6.155
plots                    5.706  0.078   5.925
ExposureSurvival         5.102  0.050   5.203
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/signeR.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘signeR’ ...
** this is package ‘signeR’ version ‘2.12.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++14
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -DARMA_USE_CURRENT -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -DARMA_USE_CURRENT -fPIC  -falign-functions=64 -Wall -g -O2   -c fuzzy.cpp -o fuzzy.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include   -DARMA_USE_CURRENT -fPIC  -falign-functions=64 -Wall -g -O2   -c gibbs_2.cpp -o gibbs_2.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c signeR_init.c -o signeR_init.o
clang++ -arch x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o signeR.so RcppExports.o fuzzy.o gibbs_2.o signeR_init.o -Wl,-S -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-signeR/00new/signeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (signeR)