系统环境 #

我目前使用的是LMDE（基于Debian的发行版，类似Ubuntu），R版本信息如下：

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: LMDE 5 (elsie)

问题描述 #

我在安装R包时经常遇到错误，试过一些本地解决方案（比如安装依赖包、升级版本、从GitHub安装等）但大多无效。最近尝试安装rms包一直失败，以下是我试过的方法及对应的日志。

尝试过的安装方法及日志 #

尝试1：使用pacman安装 #

执行命令：

if (!require("pacman"))
install.packages("pacman")
pacman::p_install(rms)

安装日志：

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependency ‘Hmisc’
"download"
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcn.f -o cidxcn.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcp.f -o cidxcp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c hoeffd.f -o hoeffd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c jacklins.f -o jacklins.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c largrec.f -o largrec.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c rcorr.f -o rcorr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c string_box.c -o string_box.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c wclosest.f -o wclosest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Hmisc/00new/Hmisc/libs
** R
Error in parse(outFile) :
/tmp/Rtmp2kS6VC/R.INSTALL3a165bca1f38/Hmisc/R/movStats.r:398:43: unexpected '>'
397:             else
398:               info <- knitr::kable(info) |>
^
ERROR: unable to collate and parse R files for package ‘Hmisc’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/Hmisc’
* installing *source* package ‘rms’ ...
** package ‘rms’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c lrmfit.f -o lrmfit.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c mlmats.f -o mlmats.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c ormuv.f -o ormuv.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c robcovf.f -o robcovf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rms.so init.o lrmfit.o mlmats.o ormuv.o robcovf.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-rms/00new/rms/libs
** R
Error in parse(outFile) :
/tmp/RtmpsUMuRd/R.INSTALL3a5392a2cc/rms/R/latex.cph.s:56:49: unexpected '>'
55:       knitr::kable(s, format='html',
56:                    align='r', row.names=FALSE) |>
^
ERROR: unable to collate and parse R files for package ‘rms’
* removing ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0/rms’
The downloaded source packages are in
‘/tmp/RtmpUQQ6Hn/downloaded_packages’
Warning messages:
1: In utils::install.packages(package, ...) :
installation of package ‘Hmisc’ had non-zero exit status
2: In utils::install.packages(package, ...) :
installation of package ‘rms’ had non-zero exit status
3: In pacman::p_install(rms) :

尝试2：直接使用install.packages安装 #

执行命令：

install.packages("rms")

安装日志：

Installing package into ‘/home/r/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rvest’, ‘svglite’, ‘Hmisc’, ‘kableExtra’
trying URL 'https://cloud.r-project.org/src/contrib/rvest_1.0.3.tar.gz'
"download"
* installing *source* package ‘rvest’ ...
** package ‘rvest’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (rvest)
* installing *source* package ‘svglite’ ...
** package ‘svglite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/r/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I'/usr/lib/R/site-library/systemfonts/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/r/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I'/usr/lib/R/site-library/systemfonts/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c devSVG.cpp -o devSVG.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o svglite.so cpp11.o devSVG.o -lpng -lz -L/usr/lib/R/lib -lR
installing to /home/r/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-svglite/00new/svglite/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 (svglite)
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcn.f -o cidxcn.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c cidxcp.f -o cidxcp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c hoeffd.f -o hoeffd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c jacklins.f -o jacklins.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c largrec.f -o largrec.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong  -c maxempr.f -o maxempr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-XqSJAD/r-base-4.0.