[ Started: 2024-05-17 15:20:17 CEST ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [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/openssl_2.2.0.tar.gz' Content type 'application/x-gzip' length 1207404 bytes (1.2 MB) ================================================== downloaded 1.2 MB * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3 ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c aes.c -o aes.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base64.c -o base64.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bignum.c -o bignum.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cert.c -o cert.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compatibility.c -o compatibility.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c diffie.c -o diffie.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c envelope.c -o envelope.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c error.c -o error.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hash.c -o hash.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c info.c -o info.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c keygen.c -o keygen.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c keys.c -o keys.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c onload.c -o onload.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c openssh.c -o openssh.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c password.c -o password.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pbkdf.c -o pbkdf.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pem.c -o pem.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pkcs12.c -o pkcs12.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pkcs7.c -o pkcs7.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rand.c -o rand.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rsa.c -o rsa.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c signing.c -o signing.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ssl.c -o ssl.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stream.c -o stream.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c x25519.c -o x25519.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bcrypt/blowfish.c -o bcrypt/blowfish.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-openssl/00new/openssl/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 (openssl) The downloaded source packages are in ‘/tmp/RtmpLFj3HF/downloaded_packages’ Bioconductor version '3.18' is out-of-date; the current release version '3.19' is available with R version '4.4'; 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 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29) Old packages: 'broom', 'rmarkdown', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/broom_1.0.6.tar.gz' Content type 'application/x-gzip' length 641538 bytes (626 KB) ================================================== downloaded 626 KB trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.27.tar.gz' Content type 'application/x-gzip' length 2190416 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/wppi_1.10.0.tar.gz' Content type 'application/gzip' length 662114 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘broom’ ... ** package ‘broom’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (broom) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-05-17 15:20:46] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 15:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:46] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Contains 1 files. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 15:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-17 15:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-17 15:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-17 15:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-17 15:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-17 15:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:46] [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 [2024-05-17 15:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 15:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Contains 1 files. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 15:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-17 15:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-17 15:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-17 15:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-17 15:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-17 15:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-17 15:20:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 15:20:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:50] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Contains 1 files. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-17 15:20:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-17 15:20:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-17 15:20:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-17 15:20:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-17 15:20:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-17 15:20:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-17 15:20:50] [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/RtmpLFj3HF/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 1.30.23), R 4.3.3 (2024-02-29) 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: rmarkdown, BiocStyle [ Finished: 2024-05-17 15:20:58 CEST ]