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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:signeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings signeR_2.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/signeR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signeR’ version ‘2.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 48 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: 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 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 ... NOTE
covariate: no visible binding for global variable ‘.’
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’
genCountMatrixFromVcf: no visible global function definition for
  ‘alt<-’
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 alt<- exposure fc
  project sig sig_test
* 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      45.897  0.597  60.975
ExposureSurvModel       13.818  0.214  16.180
ExposureClassify        12.366  0.358  16.856
ExposureFuzzyClustering 10.396  0.061  15.099
Diffexp                  4.163  0.128   8.067
ExposureSurvival         3.333  0.068   5.947
genMatrix                3.306  0.014   5.311
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/signeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL signeR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘signeR’ ...
** this is package ‘signeR’ version ‘2.11.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c fuzzy.cpp -o fuzzy.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from fuzzy.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
fuzzy.cpp: In function ‘Rcpp::List FuzzyClusterCpp(arma::cube, arma::mat, int, int, double)’:
fuzzy.cpp:143:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  143 |       if(C>=j) C = j-1;
      |          ~^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gibbs_2.cpp -o gibbs_2.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from gibbs_2.cpp:5:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c signeR_init.c -o signeR_init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o signeR.so RcppExports.o fuzzy.o gibbs_2.o signeR_init.o -Wl,-S -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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)