[ Started: 2023-11-06 19:25:13 CET ]
[ progeny v1.17.3 for BioC-3.17 from https://github.com/saezlab/progeny@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/usr/lib/R/library"             
Bioconductor version '3.17' is out-of-date; the current release version '3.18'
  is available with R version '4.3'; see https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
SparseArray (1.2.0 -> 1.2.1) [CRAN]
Installing 1 packages: SparseArray
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.1.tar.gz'
Content type 'application/x-gzip' length 366888 bytes (358 KB)
==================================================
downloaded 358 KB

* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Rvector_summarization.c -o Rvector_summarization.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Rvector_utils.c -o Rvector_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SBT_utils.c -o SBT_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_abind.c -o SparseArray_abind.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_class.c -o SparseArray_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SparseMatrix_mult.c -o SparseMatrix_mult.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c coerceVector2.c -o coerceVector2.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c leaf_vector_Arith.c -o leaf_vector_Arith.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c leaf_vector_Compare.c -o leaf_vector_Compare.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c leaf_vector_Logic.c -o leaf_vector_Logic.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c leaf_vector_summarization.c -o leaf_vector_summarization.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c leaf_vector_utils.c -o leaf_vector_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c matrixStats_methods.c -o matrixStats_methods.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c randomSparseArray.c -o randomSparseArray.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c readSparseCSV.c -o readSparseCSV.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c rowsum_methods.c -o rowsum_methods.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c test.c -o test.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -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 -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray)

The downloaded source packages are in
	‘/tmp/Rtmp60HWhv/downloaded_packages’
[ Finished: 2023-11-06 19:25:41 CET ]