ERROR: loading failed * removing ‘/home/dean/R/x86_64-pc-linux-gnu-library/4.1/sybilSBML’ #196
Description
I would like to simulate a community of bacteria using BacArena. I reconstructed the genome-scale metabolic networks of the bacteria using gapseq. I now would like to import those models and add them in the Arena to run the cross-feeding experiment. This is my code:
note:libsbml (5.18.0)。
'remotes::install_github("SysBioChalmers/sybil-SBML")'
"'Using GitHub PAT from the git credential store.
Downloading GitHub repo SysBioChalmers/sybil-SBML@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
checking for file ‘/tmp/RtmpnMh85w/remotes17b926807db6/SysBioChalmers-sybil-S✔ checking for file ‘/tmp/RtmpnMh85w/remotes17b926807db6/SysBioChalmers-sybil-SBML-8756890/DESCRIPTION’
─ preparing ‘sybilSBML’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
✔ checking vignette meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘sybilSBML_3.1.3.tar.gz’
将程序包安装入‘/home/dean/R/x86_64-pc-linux-gnu-library/4.1’
(因为‘lib’没有被指定)
- installing source package ‘sybilSBML’ ...
** using staged installation
checking for gcc... gcc
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for pkg-config... /usr/bin/pkg-config
configure: pkg-config file for libSBML is not available
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sbml/SBMLTypes.h usability... yes
checking sbml/SBMLTypes.h presence... yes
checking for sbml/SBMLTypes.h... yes
checking for library containing readSBML... none required
checking for readSBML in -lsbml... yes
checking for sbml/packages/fbc/common/FbcExtensionTypes.h... yes
checking for sbml/packages/groups/common/GroupsExtensionTypes.h... yes
checking for SBase_getPlugin... yes
checking for SBMLExtensionRegistry_getRegisteredPackages... yes
checking for GeneProductAssociation_setAssociation... yes
checking for FbcReactionPlugin_getLowerFluxBound... yes
configure: creating ./config.status
config.status: creating src/Makevars.tmp
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sbml.c -o sbml.o
gcc -I"/usr/share/R/include" -DNDEBUG -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -ffile-prefix-map=/build/r-base-4A2Reg/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sybilSBML.c -o sybilSBML.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sybilSBML.so init.o sbml.o sybilSBML.o -L/usr/local/lib -L/usr/lib -L/usr/lib64 -lsbml -L/usr/lib/R/lib -lR
installing to /home/dean/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-sybilSBML/00new/sybilSBML/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
Error: package or namespace load failed for ‘sybilSBML’ in dyn.load(file, DLLpath = DLLpath, ...):
无法载入共享目标对象‘/home/dean/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-sybilSBML/00new/sybilSBML/libs/sybilSBML.so’：:
libsbml.so.5: 无法打开共享目标文件: 没有那个文件或目录
错误: loading failed
停止执行
ERROR: loading failed - removing ‘/home/dean/R/x86_64-pc-linux-gnu-library/4.1/sybilSBML’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpnMh85w/file17b957933e79/sybilSBML_3.1.3.tar.gz’ had non-zero exit status"'
My question is: Can I simulate in BacArena, How should I install sybilSBML?