[ Started: 2025-05-31 02:17:51 CEST ]
[ 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"             
Bioconductor version '3.20' is out-of-date; the current release version '3.21'
  is available with R version '4.5'; 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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Old packages: 'haven', 'statnet.common'
trying URL 'https://cloud.r-project.org/src/contrib/haven_2.5.5.tar.gz'
Content type 'application/x-gzip' length 316909 bytes (309 KB)
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downloaded 309 KB

trying URL 'https://cloud.r-project.org/src/contrib/statnet.common_4.12.0.tar.gz'
Content type 'application/x-gzip' length 86582 bytes (84 KB)
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downloaded 84 KB

* installing *source* package ‘haven’ ...
** package ‘haven’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lz 
** 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’
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 tagged_na.c -o tagged_na.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/CKHashTable.c -o readstat/CKHashTable.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_bits.c -o readstat/readstat_bits.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_convert.c -o readstat/readstat_convert.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_error.c -o readstat/readstat_error.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_io_unistd.c -o readstat/readstat_io_unistd.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_malloc.c -o readstat/readstat_malloc.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_metadata.c -o readstat/readstat_metadata.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_parser.c -o readstat/readstat_parser.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_value.c -o readstat/readstat_value.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_variable.c -o readstat/readstat_variable.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/readstat_writer.c -o readstat/readstat_writer.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/ieee.c -o readstat/sas/ieee.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_sas.c -o readstat/sas/readstat_sas.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_sas7bcat_read.c -o readstat/sas/readstat_sas7bcat_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_sas7bcat_write.c -o readstat/sas/readstat_sas7bcat_write.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_sas7bdat_read.c -o readstat/sas/readstat_sas7bdat_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_sas7bdat_write.c -o readstat/sas/readstat_sas7bdat_write.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_sas_rle.c -o readstat/sas/readstat_sas_rle.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_xport.c -o readstat/sas/readstat_xport.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_xport_parse_format.c -o readstat/sas/readstat_xport_parse_format.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_xport_read.c -o readstat/sas/readstat_xport_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/sas/readstat_xport_write.c -o readstat/sas/readstat_xport_write.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_por.c -o readstat/spss/readstat_por.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_por_parse.c -o readstat/spss/readstat_por_parse.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_por_read.c -o readstat/spss/readstat_por_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_por_write.c -o readstat/spss/readstat_por_write.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav.c -o readstat/spss/readstat_sav.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav_compress.c -o readstat/spss/readstat_sav_compress.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav_parse.c -o readstat/spss/readstat_sav_parse.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav_parse_mr_name.c -o readstat/spss/readstat_sav_parse_mr_name.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav_parse_timestamp.c -o readstat/spss/readstat_sav_parse_timestamp.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav_read.c -o readstat/spss/readstat_sav_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_sav_write.c -o readstat/spss/readstat_sav_write.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_spss.c -o readstat/spss/readstat_spss.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_spss_parse.c -o readstat/spss/readstat_spss_parse.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_zsav_compress.c -o readstat/spss/readstat_zsav_compress.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_zsav_read.c -o readstat/spss/readstat_zsav_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/spss/readstat_zsav_write.c -o readstat/spss/readstat_zsav_write.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/stata/readstat_dta.c -o readstat/stata/readstat_dta.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/stata/readstat_dta_parse_timestamp.c -o readstat/stata/readstat_dta_parse_timestamp.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/stata/readstat_dta_read.c -o readstat/stata/readstat_dta_read.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 readstat/stata/readstat_dta_write.c -o readstat/stata/readstat_dta_write.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 DfReader.cpp -o DfReader.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 DfWriter.cpp -o DfWriter.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/cpp11/include'    -Ireadstat -DHAVE_ZLIB -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 haven_types.cpp -o haven_types.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o haven.so tagged_na.o readstat/CKHashTable.o readstat/readstat_bits.o readstat/readstat_convert.o readstat/readstat_error.o readstat/readstat_io_unistd.o readstat/readstat_malloc.o readstat/readstat_metadata.o readstat/readstat_parser.o readstat/readstat_value.o readstat/readstat_variable.o readstat/readstat_writer.o readstat/sas/ieee.o readstat/sas/readstat_sas.o readstat/sas/readstat_sas7bcat_read.o readstat/sas/readstat_sas7bcat_write.o readstat/sas/readstat_sas7bdat_read.o readstat/sas/readstat_sas7bdat_write.o readstat/sas/readstat_sas_rle.o readstat/sas/readstat_xport.o readstat/sas/readstat_xport_parse_format.o readstat/sas/readstat_xport_read.o readstat/sas/readstat_xport_write.o readstat/spss/readstat_por.o readstat/spss/readstat_por_parse.o readstat/spss/readstat_por_read.o readstat/spss/readstat_por_write.o readstat/spss/readstat_sav.o readstat/spss/readstat_sav_compress.o readstat/spss/readstat_sav_parse.o readstat/spss/readstat_sav_parse_mr_name.o readstat/spss/readstat_sav_parse_timestamp.o readstat/spss/readstat_sav_read.o readstat/spss/readstat_sav_write.o readstat/spss/readstat_spss.o readstat/spss/readstat_spss_parse.o readstat/spss/readstat_zsav_compress.o readstat/spss/readstat_zsav_read.o readstat/spss/readstat_zsav_write.o readstat/stata/readstat_dta.o readstat/stata/readstat_dta_parse_timestamp.o readstat/stata/readstat_dta_read.o readstat/stata/readstat_dta_write.o DfReader.o DfWriter.o cpp11.o haven_types.o -lz -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-haven/00new/haven/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 (haven)
* installing *source* package ‘statnet.common’ ...
** package ‘statnet.common’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -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
gcc -I"/usr/share/R/include" -DNDEBUG       -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 logspace_utils.c -o logspace_utils.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o statnet.common.so init.o logspace_utils.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-statnet.common/00new/statnet.common/libs
** 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
** 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 (statnet.common)

The downloaded source packages are in
	‘/tmp/RtmpHXT3hq/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 1 packages ahead of CRAN: BiocStyle
[ Finished: 2025-05-31 02:18:25 CEST ]