[ Started: 2024-04-30 15:18:59 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4"      "/opt/R-alpha/lib/R/library"     
Warning message:
package ‘remotes’ was built under R version 4.5.0 
Warning message:
package ‘BiocManager’ was built under R version 4.5.0 
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04
  r86334)
Old packages: 'edgeR', 'SparseArray', 'wppi'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/edgeR_4.1.31.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SparseArray_1.3.7.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz'
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* installing *source* package ‘edgeR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_add_prior_count.cpp -o R_add_prior_count.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_compute_apl.cpp -o R_compute_apl.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_fit_levenberg.cpp -o R_fit_levenberg.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_fit_one_group.cpp -o R_fit_one_group.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_ql_glm.c -o R_ql_glm.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c add_prior.cpp -o add_prior.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c adj_coxreid.cpp -o adj_coxreid.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c fmm_spline.c -o fmm_spline.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c glm_levenberg.cpp -o glm_levenberg.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c glm_one_group.cpp -o glm_one_group.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c init.cpp -o init.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c interpolator.cpp -o interpolator.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c nbdev.c -o nbdev.o
g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c objects.cpp -o objects.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c ql_glm.c -o ql_glm.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c ql_weights.c -o ql_weights.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c qr_hat.c -o qr_hat.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_ql_glm.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o ql_glm.o ql_weights.o qr_hat.o -llapack -L/opt/R-alpha/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-edgeR/00new/edgeR/libs
** R
** 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 (edgeR)
* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c Rvector_summarization.c -o Rvector_summarization.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c Rvector_utils.c -o Rvector_utils.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SBT_utils.c -o SBT_utils.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_abind.c -o SparseArray_abind.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_class.c -o SparseArray_class.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c SparseMatrix_mult.c -o SparseMatrix_mult.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c coerceVector2.c -o coerceVector2.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c leaf_vector_Arith.c -o leaf_vector_Arith.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c leaf_vector_Compare.c -o leaf_vector_Compare.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c leaf_vector_Logic.c -o leaf_vector_Logic.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c leaf_vector_summarization.c -o leaf_vector_summarization.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c leaf_vector_utils.c -o leaf_vector_utils.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c matrixStats_methods.c -o matrixStats_methods.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c randomSparseArray.c -o randomSparseArray.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c readSparseCSV.c -o readSparseCSV.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c rowsum_methods.c -o rowsum_methods.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c test.c -o test.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -c thread_control.c -o thread_control.o
gcc -shared -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o XVector_stubs.o coerceVector2.o leaf_vector_Arith.o leaf_vector_Compare.o leaf_vector_Logic.o leaf_vector_dotprod.o leaf_vector_summarization.o leaf_vector_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-SparseArray/00new/SparseArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package ‘BiocGenerics’ was built under R version 4.5.0 
2: package ‘abind’ was built under R version 4.5.0 
3: package ‘IRanges’ was built under R version 4.5.0 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package ‘BiocGenerics’ was built under R version 4.5.0
Warning: package ‘abind’ was built under R version 4.5.0
Warning: package ‘IRanges’ was built under R version 4.5.0
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: package ‘BiocGenerics’ was built under R version 4.5.0
Warning: package ‘abind’ was built under R version 4.5.0
Warning: package ‘IRanges’ was built under R version 4.5.0
** testing if installed package keeps a record of temporary installation path
* DONE (SparseArray)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-04-30 15:20:41] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:41] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:41] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:43] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-30 15:20:45] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

The downloaded source packages are in
	‘/tmp/RtmpcZkhwR/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04
  r86334)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 1 packages ahead of CRAN: BiocStyle
[ Finished: 2024-04-30 15:20:47 CEST ]