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R CMD BUILD
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* checking for file TraianProt/DESCRIPTION ... OK
* preparing TraianProt:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
-----------------------------------
* installing *source* package TraianProt ...
** this is package TraianProt version 0.99.8
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called rsconnect
Bioconductor version 3.23 (BiocManager 1.30.27), R 4.6.0 alpha (2026-04-05
r89794)
Installing package(s) 'rsconnect'
also installing the dependencies PKI, packrat, snowflakeauth
trying URL 'https://cloud.r-project.org/src/contrib/PKI_0.1-15.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/packrat_0.9.3.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/snowflakeauth_0.2.2.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/rsconnect_1.7.0.tar.gz'
* installing *source* package PKI ...
** this is package PKI version 0.1-15
** package PKI successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... yes
checking whether it knows about openssl... yes
configure: CFLAGS:
configure: LIBS: -lssl -lcrypto
checking for gcc... gcc -std=gnu2x
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for openssl/ssl.h... yes
checking for openssl/rsa.h... yes
checking for library containing RSA_generate_key_ex... none required
checking for openssl/ssl.h... (cached) yes
checking for library containing SSL_CTX_load_verify_locations... none required
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
using C compiler: gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c asn1.c -o asn1.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pem.c -o pem.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pgp.c -o pgp.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pki-x509.c -o pki-x509.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c register.c -o register.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tools.c -o tools.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o PKI.so asn1.o init.o pem.o pgp.o pki-x509.o register.o tools.o -lssl -lcrypto -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /tmp/Rtmp4BklMB/Rinstdc47f2c5afb87/00LOCK-TraianProt/00new/00LOCK-PKI/00new/PKI/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
ERROR: hard-coded installation path: please report to the package maintainer and use --no-staged-install
* removing /tmp/Rtmp4BklMB/Rinstdc47f2c5afb87/00LOCK-TraianProt/00new/PKI
Warning in install.packages(...) :
installation of package PKI had non-zero exit status
* installing *source* package packrat ...
** this is package packrat version 0.9.3
** package packrat 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
ERROR: hard-coded installation path: please report to the package maintainer and use --no-staged-install
* removing /tmp/Rtmp4BklMB/Rinstdc47f2c5afb87/00LOCK-TraianProt/00new/packrat
Warning in install.packages(...) :
installation of package packrat had non-zero exit status
* installing *source* package snowflakeauth ...
** this is package snowflakeauth version 0.2.2
** package snowflakeauth successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
ERROR: hard-coded installation path: please report to the package maintainer and use --no-staged-install
* removing /tmp/Rtmp4BklMB/Rinstdc47f2c5afb87/00LOCK-TraianProt/00new/snowflakeauth
Warning in install.packages(...) :
installation of package snowflakeauth had non-zero exit status
ERROR: dependencies PKI, packrat, snowflakeauth are not available for package rsconnect
Perhaps try a variation of:
install.packages(c('PKI', 'packrat', 'snowflakeauth'))
* removing /tmp/Rtmp4BklMB/Rinstdc47f2c5afb87/00LOCK-TraianProt/00new/rsconnect
Warning in install.packages(...) :
installation of package rsconnect had non-zero exit status
The downloaded source packages are in
/tmp/RtmpvPykHh/downloaded_packages
Error in library(rsconnect) : there is no package called rsconnect
Error: unable to load R code in package TraianProt
Execution halted
ERROR: lazy loading failed for package TraianProt
* removing /tmp/Rtmp4BklMB/Rinstdc47f2c5afb87/TraianProt
-----------------------------------
ERROR: package installation failed