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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_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/signeR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signeR’ version ‘2.10.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘signeR’
See ‘/home/biocbuild/bbs-3.21-bioc/meat/signeR.Rcheck/00install.out’ for details.
* 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      9.546  0.209  10.831
ExposureFuzzyClustering 9.228  0.093   9.727
ExposureClassify        5.723  0.258   6.419
ExposureSurvModel       5.783  0.116   7.049
Diffexp                 4.536  0.139   5.157
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘signeR’ ...
** this is package ‘signeR’ version ‘2.10.0’
** 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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c fuzzy.cpp -o fuzzy.o
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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gibbs_2.cpp -o gibbs_2.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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/lib -L/usr/local/lib -o signeR.so RcppExports.o fuzzy.o gibbs_2.o signeR_init.o -Wl,-S -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-signeR/00new/signeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘signeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘signeR’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘signeR’
** testing if installed package keeps a record of temporary installation path
* DONE (signeR)