[ Started: 2025-03-01 00:10:09 CET ]
[ CARNIVAL v2.16.0 for BioC-3.20 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_20 (a7305b3 2024-10-29 10:46:30) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4"      "/usr/lib/R/library"             
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Old packages: 'segmented', 'xml2'
trying URL 'https://cloud.r-project.org/src/contrib/segmented_2.1-4.tar.gz'
Content type 'application/x-gzip' length 311459 bytes (304 KB)
==================================================
downloaded 304 KB

trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.7.tar.gz'
Content type 'application/x-gzip' length 152691 bytes (149 KB)
==================================================
downloaded 149 KB

* installing *source* package ‘segmented’ ...
** package ‘segmented’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** 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 (segmented)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-lxml2
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c connection.cpp -o connection.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP      -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c init.c -o init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_doc.cpp -o xml2_doc.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP      -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c xml2_init.c -o xml2_init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_namespace.cpp -o xml2_namespace.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_node.cpp -o xml2_node.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_output.cpp -o xml2_output.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_schema.cpp -o xml2_schema.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_url.cpp -o xml2_url.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP     -fvisibility=hidden -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c xml2_xpath.cpp -o xml2_xpath.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -lxml2 -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-xml2/00new/xml2/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 (xml2)

The downloaded source packages are in
	‘/tmp/RtmpRqyWqI/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 2 packages ahead of CRAN: xml2, BiocStyle
[ Finished: 2025-03-01 00:10:40 CET ]