[ Started: 2024-03-16 11:51:55 CET ]
[ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.18"
[3] "/home/omnipath/local/R/4.3"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/sass_0.4.9.tar.gz'
Content type 'application/x-gzip' length 3025086 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

* installing *source* package ‘sass’ ...
** package ‘sass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/share/R/share/make/shlib.mk:18: warning: overriding recipe for target 'shlib-clean'
Makevars:12: warning: ignoring old recipe for target 'shlib-clean'
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’
/usr/share/R/share/make/shlib.mk:18: warning: overriding recipe for target 'shlib-clean'
Makevars:12: warning: ignoring old recipe for target 'shlib-clean'
gcc -I"/usr/share/R/include" -DNDEBUG -I./libsass/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 compile.c -o compile.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libsass/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 init.cpp -o init.o
MAKEFLAGS= CC="gcc" CFLAGS="-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 " CXX="g++ -std=gnu++17" AR="ar" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro" make -C libsass
make[1]: Entering directory '/tmp/RtmppsfLgs/R.INSTALL319a2519a5f34c/sass/src/libsass'
gcc -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  -O2 -I ./include  -fPIC -c -o src/cencode.o src/cencode.c
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast.o src/ast.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_values.o src/ast_values.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_supports.o src/ast_supports.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_sel_super.o src/ast_sel_super.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_selectors.o src/ast_selectors.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/context.o src/context.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/constants.o src/constants.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_utils.o src/fn_utils.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_miscs.o src/fn_miscs.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_maps.o src/fn_maps.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_lists.o src/fn_lists.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_colors.o src/fn_colors.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_numbers.o src/fn_numbers.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_strings.o src/fn_strings.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/fn_selectors.o src/fn_selectors.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/color_maps.o src/color_maps.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/environment.o src/environment.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/bind.o src/bind.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/file.o src/file.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/util.o src/util.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/util_string.o src/util_string.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/json.o src/json.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/units.o src/units.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/values.o src/values.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/plugins.o src/plugins.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/source.o src/source.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/position.o src/position.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/lexer.o src/lexer.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/parser.o src/parser.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/parser_selectors.o src/parser_selectors.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/prelexer.o src/prelexer.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/eval.o src/eval.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/eval_selectors.o src/eval_selectors.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/expand.o src/expand.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/listize.o src/listize.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/cssize.o src/cssize.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/extender.o src/extender.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/extension.o src/extension.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/stylesheet.o src/stylesheet.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/output.o src/output.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/inspect.o src/inspect.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/emitter.o src/emitter.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/check_nesting.o src/check_nesting.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/remove_placeholders.o src/remove_placeholders.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/sass.o src/sass.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/sass_values.o src/sass_values.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/sass_context.o src/sass_context.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/sass_functions.o src/sass_functions.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/sass2scss.o src/sass2scss.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/backtrace.o src/backtrace.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/operators.o src/operators.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/ast2c.o src/ast2c.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/c2ast.o src/c2ast.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/to_value.o src/to_value.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/source_map.o src/source_map.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/error_handling.o src/error_handling.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/memory/allocator.o src/memory/allocator.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/utf8_string.o src/utf8_string.cpp
g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include  -fPIC -c -o src/base64vlq.o src/base64vlq.cpp
mkdir lib
ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o
a - src/cencode.o
a - src/ast.o
a - src/ast_values.o
a - src/ast_supports.o
a - src/ast_sel_cmp.o
a - src/ast_sel_unify.o
a - src/ast_sel_super.o
a - src/ast_sel_weave.o
a - src/ast_selectors.o
a - src/context.o
a - src/constants.o
a - src/fn_utils.o
a - src/fn_miscs.o
a - src/fn_maps.o
a - src/fn_lists.o
a - src/fn_colors.o
a - src/fn_numbers.o
a - src/fn_strings.o
a - src/fn_selectors.o
a - src/color_maps.o
a - src/environment.o
a - src/ast_fwd_decl.o
a - src/bind.o
a - src/file.o
a - src/util.o
a - src/util_string.o
a - src/json.o
a - src/units.o
a - src/values.o
a - src/plugins.o
a - src/source.o
a - src/position.o
a - src/lexer.o
a - src/parser.o
a - src/parser_selectors.o
a - src/prelexer.o
a - src/eval.o
a - src/eval_selectors.o
a - src/expand.o
a - src/listize.o
a - src/cssize.o
a - src/extender.o
a - src/extension.o
a - src/stylesheet.o
a - src/output.o
a - src/inspect.o
a - src/emitter.o
a - src/check_nesting.o
a - src/remove_placeholders.o
a - src/sass.o
a - src/sass_values.o
a - src/sass_context.o
a - src/sass_functions.o
a - src/sass2scss.o
a - src/backtrace.o
a - src/operators.o
a - src/ast2c.o
a - src/c2ast.o
a - src/to_value.o
a - src/source_map.o
a - src/error_handling.o
a - src/memory/allocator.o
a - src/memory/shared_ptr.o
a - src/utf8_string.o
a - src/base64vlq.o
make[1]: Leaving directory '/tmp/RtmppsfLgs/R.INSTALL319a2519a5f34c/sass/src/libsass'
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sass.so compile.o init.o ./libsass/lib/libsass.a -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-sass/00new/sass/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (sass)

The downloaded source packages are in
	‘/tmp/RtmpmIpy8b/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Old packages: 'Biostrings', 'tinytex', 'zlibbioc'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biostrings_2.70.3.tar.gz'
Content type 'application/x-gzip' length 12740728 bytes (12.2 MB)
==================================================
downloaded 12.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/tinytex_0.50.tar.gz'
Content type 'application/x-gzip' length 34312 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/zlibbioc_1.48.2.tar.gz'
Content type 'application/x-gzip' length 382668 bytes (373 KB)
==================================================
downloaded 373 KB

* installing *source* package ‘Biostrings’ ...
** 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/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 BAB_class.c -o BAB_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 BitMatrix.c -o BitMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 MIndex_class.c -o MIndex_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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_Biostrings.c -o R_init_Biostrings.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 SparseList_utils.c -o SparseList_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 XStringSet_class.c -o XStringSet_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 XString_class.c -o XString_class.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 align_needwunsQS.c -o align_needwunsQS.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 align_utils.c -o align_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 find_palindromes.c -o find_palindromes.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 gtestsim.c -o gtestsim.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 inject_code.c -o inject_code.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 letter_frequency.c -o letter_frequency.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_PWM.c -o match_PWM.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pattern.c -o match_pattern.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pattern_indels.c -o match_pattern_indels.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pdict.c -o match_pdict.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_pdict_utils.c -o match_pdict_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 match_reporting.c -o match_reporting.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 matchprobes.c -o matchprobes.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 pmatchPattern.c -o pmatchPattern.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 read_fasta_files.c -o read_fasta_files.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 read_fastq_files.c -o read_fastq_files.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 replaceAt.c -o replaceAt.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 replace_letter_at.c -o replace_letter_at.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 strutils.c -o strutils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 translate.c -o translate.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 utils.c -o utils.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/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 xscat.c -o xscat.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘pattern’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** 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 (Biostrings)
* installing *source* package ‘tinytex’ ...
** package ‘tinytex’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tinytex)
* installing *source* package ‘zlibbioc’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
mkdir -p "/home/omnipath/local/R/4.3-3.18/00LOCK-zlibbioc/00new/zlibbioc/include"
gcc -I"/usr/share/R/include" -DNDEBUG       -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_zlibbioc.c -o R_init_zlibbioc.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o zlibbioc.so R_init_zlibbioc.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-zlibbioc/00new/zlibbioc/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 (zlibbioc)

The downloaded source packages are in
	‘/tmp/RtmpmIpy8b/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (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' 

Skipping 1 packages ahead of CRAN: tinytex
[ Finished: 2024-03-16 11:54:07 CET ]