为什么R包`qtlbim`在本地安装失败，但在docker容器安装成功？

Question

我很难理解为什么在运行docker rocker容器时可以安装来自Github的R包qtlbim，而在我的桌面(docker外部)运行R时却无法安装相同的包。

当我在rocker容器中运行R时，我在终端中看到了这一点：

remotes::install_github("fboehm/qtlbim")
Downloading GitHub repo fboehm/qtlbim@HEAD
Running `R CMD build`...
* checking for file ‘/tmp/Rtmprg1Xz8/remotes1086cb13f8a/fboehm-qtlbim-d9077cf/DESCRIPTION’ ... OK
* preparing ‘qtlbim’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘qtlbim_2.0.7.tar.gz’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘qtlbim’ ...
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c GlobalVars.c -o GlobalVars.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c GlobalVars_SingleTrait.c -o GlobalVars_SingleTrait.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MatrixUtils.c -o MatrixUtils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MultipleTraitsMCMC.c -o MultipleTraitsMCMC.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RMultipleTraitsMCMCSetup.c -o RMultipleTraitsMCMCSetup.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ROutputManager.c -o ROutputManager.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RSingleTraitMCMCSetup.c -o RSingleTraitMCMCSetup.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SingleTraitMCMC.c -o SingleTraitMCMC.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SingleTraitMCMCSamplingRoutines.c -o SingleTraitMCMCSamplingRoutines.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c StatUtils.c -o StatUtils.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o qtlbim.so GlobalVars.o GlobalVars_SingleTrait.o MatrixUtils.o MultipleTraitsMCMC.o RMultipleTraitsMCMCSetup.o ROutputManager.o RSingleTraitMCMCSetup.o SingleTraitMCMC.o SingleTraitMCMCSamplingRoutines.o StatUtils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-qtlbim/00new/qtlbim/libs
** R
** data
** demo
** 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 (qtlbim)

但是当我尝试在docker外部的R会话中安装时，我看到了这一点：

remotes::install_github("CRAN/qtlbim")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo CRAN/qtlbim@HEAD
✓  checking for file ‘/tmp/RtmpUF0v2l/remotes34e8051627d66/cran-qtlbim-afb635d/DESCRIPTION’ ...
─  preparing ‘qtlbim’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘qtlbim_2.0.7.tar.gz’
   
Installing package into ‘/home/fred/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘qtlbim’ ...
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c GlobalVars.c -o GlobalVars.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c GlobalVars_SingleTrait.c -o GlobalVars_SingleTrait.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MatrixUtils.c -o MatrixUtils.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MultipleTraitsMCMC.c -o MultipleTraitsMCMC.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RMultipleTraitsMCMCSetup.c -o RMultipleTraitsMCMCSetup.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ROutputManager.c -o ROutputManager.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RSingleTraitMCMCSetup.c -o RSingleTraitMCMCSetup.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SingleTraitMCMC.c -o SingleTraitMCMC.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SingleTraitMCMCSamplingRoutines.c -o SingleTraitMCMCSamplingRoutines.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3BoT6Y/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c StatUtils.c -o StatUtils.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o qtlbim.so GlobalVars.o GlobalVars_SingleTrait.o MatrixUtils.o MultipleTraitsMCMC.o RMultipleTraitsMCMCSetup.o ROutputManager.o RSingleTraitMCMCSetup.o SingleTraitMCMC.o SingleTraitMCMCSamplingRoutines.o StatUtils.o -L/usr/lib/R/lib -lR
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:34: multiple definition of `Y'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:77: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:73: multiple definition of `AMU'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:30: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:43: multiple definition of `GVALUE'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:79: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:56: multiple definition of `QCHR'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:13: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:52: multiple definition of `COEF'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:9: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:83: multiple definition of `MAIN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:40: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:75: multiple definition of `GAMMA'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:32: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:95: multiple definition of `GAMMA_EPISTASIS'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:54: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:93: multiple definition of `EPISTATIC'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:52: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:103: multiple definition of `GAMMA_GBYE'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:64: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:67: multiple definition of `GBYE_FIX'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:24: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:77: multiple definition of `VE'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:34: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:87: multiple definition of `VMAIN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:44: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:97: multiple definition of `VEPISTASIS'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:56: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:105: multiple definition of `V_GBYE_FIX'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:66: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:61: multiple definition of `FIX'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:18: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:63: multiple definition of `RAN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:20: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:65: multiple definition of `VRAN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:22: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:54: multiple definition of `QLOC'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:11: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:26: multiple definition of `GENO'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:75: first defined here
/usr/bin/ld: MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:85: multiple definition of `GAMMA_MAIN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:42: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:12: multiple definition of `QTLLOC'; MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:12: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:36: multiple definition of `NPHENO'; MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:36: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:38: multiple definition of `MULTIPLE'; MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:38: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:34: multiple definition of `Y'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:77: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:14: multiple definition of `DiffLocation'; MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:14: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:87: multiple definition of `VMAIN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:44: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:97: multiple definition of `VEPISTASIS'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:56: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:105: multiple definition of `V_GBYE_FIX'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:66: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:73: multiple definition of `AMU'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:30: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:16: multiple definition of `SIGMA'; MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:16: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:83: multiple definition of `MAIN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:40: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:93: multiple definition of `EPISTATIC'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:52: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:43: multiple definition of `GVALUE'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:79: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:26: multiple definition of `GENO'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:75: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:52: multiple definition of `COEF'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:9: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:54: multiple definition of `QLOC'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:11: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:56: multiple definition of `QCHR'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:13: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:75: multiple definition of `GAMMA'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:32: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:85: multiple definition of `GAMMA_MAIN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:42: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:95: multiple definition of `GAMMA_EPISTASIS'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:54: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:61: multiple definition of `FIX'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:18: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:63: multiple definition of `RAN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:20: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:65: multiple definition of `VRAN'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:22: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:67: multiple definition of `GBYE_FIX'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:24: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:103: multiple definition of `GAMMA_GBYE'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:64: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:77: multiple definition of `VE'; GlobalVars_SingleTrait.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_SingleTrait.c:34: first defined here
/usr/bin/ld: RMultipleTraitsMCMCSetup.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:18: multiple definition of `SCALE'; MultipleTraitsMCMC.o:/tmp/RtmpBf0FKz/R.INSTALL45ef74784e70f/qtlbim/src/GlobalVars_MultipleTraits.h:18: first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: qtlbim.so] Error 1
ERROR: compilation failed for package ‘qtlbim’
* removing ‘/home/fred/R/x86_64-pc-linux-gnu-library/4.0/qtlbim’
Error: Failed to install 'qtlbim' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpUF0v2l/file34e8079f6c1f3/qtlbim_2.0.7.tar.gz’ had non-zero exit status

我想我需要修改R桌面安装的Makevars，使其与安装在docker容器中时看到的标志相匹配。有没有简单的方法可以做到这一点？如何知道标志的默认值是什么？是否有通过withr::with_makevars的单行解决方案

非常感谢你的帮助。

Answer 1

您的代码正在成为gcc更改的牺牲品，该更改将原本的警告变成了错误。简而言之，您不能再在多个“编译单元”中定义一个全局变量，而必须只定义一次，然后使用extern来引用它。(跟踪gcc和clang开发版本的Brian Ripley在2019年12月，也就是gcc-10发布前几个月，迫使所有具有类似设置的CRAN维护者进行这些更改。当默认设置更改时，我们在Debian和Ubuntu中也有类似的更改需求。这有点痛苦，但可能是值得的…)

现在，这里有一个覆盖:添加-fcommon应该会对您有所帮助。详情请参阅此页面：https://gcc.gnu.org/gcc-10/porting_to.html

编辑:确实，快速证明在这里：

edd@rob:/tmp/qtlbim(master)$ cat src/Makevars 
PKG_CFLAGS = -fcommon
edd@rob:/tmp/qtlbim(master)$ ls -l src/*so
-rwxrwxr-x 1 edd edd 191400 Jan 24 12:09 src/qtlbim.so
edd@rob:/tmp/qtlbim(master)$ lsb_release --all
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.10
Release:        20.10
Codename:       groovy
edd@rob:/tmp/qtlbim(master)$ 

R CMD INSTALL .的最后几行以

[... earlier lines and warnings omitted ...]
ccache gcc -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o qtlbim.so GlobalVars.o GlobalVars_SingleTrait.o MatrixUtils.o MultipleTraitsMCMC.o RMultipleTraitsMCMCSetup.o ROutputManager.o RSingleTraitMCMCSetup.o SingleTraitMCMC.o SingleTraitMCMCSamplingRoutines.o StatUtils.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-qtlbim/00new/qtlbim/libs
** R
** data
** demo
** 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 (qtlbim)
edd@rob:/tmp/qtlbim(master)$ 

(您可以忽略我使用的是ccache)。

编辑2:已经走到这一步了，我刚刚在你的存储库做了一个minimal PR。您可能需要对src/Makevars.win执行相同的操作，并且应该能够只复制该文件。你可以在win-builder或RHub上测试。