r - 无法在 Fedora 上安装闪亮的 R 包

问题描述

我刚刚在我的 Fedora Linux 工作站上安装了 R（版本 4.0.2），但由于某种原因我无法安装shiny它。我从终端和 RStudio 都试过了。当我尝试时： install.packages("shiny")我得到以下输出，其中似乎包含几个编译器错误：
> install.packages(c("shiny"))
Installing package into ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependencies ‘Rcpp’, ‘base64enc’, ‘httpuv’, ‘mime’, ‘jsonlite’, ‘digest’, ‘htmltools’, ‘sourcetools’, ‘later’, ‘promises’, ‘rlang’, ‘fastmap’, ‘commonmark’, ‘glue’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/Rcpp_1.0.5.tar.gz'
Content type 'application/x-gzip' length 2950521 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/base64enc_0.1-3.tar.gz'
Content type 'application/x-gzip' length 7833 bytes
==================================================
downloaded 7833 bytes

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/httpuv_1.5.4.tar.gz'
Content type 'application/x-gzip' length 1803508 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/mime_0.9.tar.gz'
Content type 'application/x-gzip' length 12843 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/jsonlite_1.7.0.tar.gz'
Content type 'application/x-gzip' length 1057524 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/digest_0.6.25.tar.gz'
Content type 'application/x-gzip' length 145642 bytes (142 KB)
==================================================
downloaded 142 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/htmltools_0.5.0.tar.gz'
Content type 'application/x-gzip' length 66001 bytes (64 KB)
==================================================
downloaded 64 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/sourcetools_0.1.7.tar.gz'
Content type 'application/x-gzip' length 24155 bytes (23 KB)
==================================================
downloaded 23 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/later_1.1.0.1.tar.gz'
Content type 'application/x-gzip' length 64221 bytes (62 KB)
==================================================
downloaded 62 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/promises_1.1.1.tar.gz'
Content type 'application/x-gzip' length 2655709 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/rlang_0.4.7.tar.gz'
Content type 'application/x-gzip' length 847308 bytes (827 KB)
==================================================
downloaded 827 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/fastmap_1.0.1.tar.gz'
Content type 'application/x-gzip' length 36802 bytes (35 KB)
==================================================
downloaded 35 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/commonmark_1.7.tar.gz'
Content type 'application/x-gzip' length 134002 bytes (130 KB)
==================================================
downloaded 130 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/glue_1.4.1.tar.gz'
Content type 'application/x-gzip' length 98581 bytes (96 KB)
==================================================
downloaded 96 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/shiny_1.5.0.tar.gz'
Content type 'application/x-gzip' length 3472148 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c api.cpp -o api.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
api.cpp:1: internal compiler error: Segmentation fault
    1 | // -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; -*-
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccemTzOV.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:176: api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/Rcpp’
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c base64.c -o base64.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
base64.c:1: internal compiler error: Segmentation fault
    1 | /* base64.c - encoding/decoding of base64
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccbjhGQf.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:167: base64.o] Error 1
ERROR: compilation failed for package ‘base64enc’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/base64enc’
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
init.c:1: internal compiler error: Segmentation fault
    1 | #include <R.h>
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccUQQysE.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:167: init.o] Error 1
ERROR: compilation failed for package ‘mime’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/mime’
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG -Iyajl/api  -I/usr/local/include  -fvisibility=hidden  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c base64.c -o base64.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
base64.c:1: internal compiler error: Segmentation fault
    1 | /*
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccXLrUUY.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:167: base64.o] Error 1
ERROR: compilation failed for package ‘jsonlite’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/jsonlite’
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c SpookyV2.cpp -o SpookyV2.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
SpookyV2.cpp:1: internal compiler error: Segmentation fault
    1 | // Spooky Hash
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccrx5YEl.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:176: SpookyV2.o] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/digest’
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include  -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Reader.cpp -o Reader.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
Reader.cpp:1: internal compiler error: Segmentation fault
    1 | #include <cstring>
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccQOxLBO.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:176: Reader.o] Error 1
ERROR: compilation failed for package ‘sourcetools’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/sourcetools’
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG -I./lib/  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c capture.c -o capture.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
capture.c:1: internal compiler error: Segmentation fault
    1 | #include <Rinternals.h>
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccHSYgy7.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:167: capture.o] Error 1
ERROR: compilation failed for package ‘rlang’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/rlang’
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -Ilib/  -I/usr/local/include  -DR_NO_REMAP -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fastmap.cpp -o fastmap.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
fastmap.cpp:1: internal compiler error: Segmentation fault
    1 | #include <R.h>
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/cc2DFAmt.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:176: fastmap.o] Error 1
ERROR: compilation failed for package ‘fastmap’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/fastmap’
* installing *source* package ‘commonmark’ ...
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/html.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions.o init.o wrapper.o commonmark.so cmark/libstatcmark.a
gcc -m64 -I"/usr/include/R" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c extensions.c -o extensions.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
extensions.c:1: internal compiler error: Segmentation fault
    1 | #include <Rinternals.h>
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccNYzNLW.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:167: extensions.o] Error 1
ERROR: compilation failed for package ‘commonmark’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/commonmark’
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c glue.c -o glue.o
*** WARNING *** there are active plugins, do not report this as a bug unless you can reproduce it without enabling any plugins.
Event                            | Plugins
PLUGIN_FINISH_UNIT               | annobin: Generate final annotations
PLUGIN_START_UNIT                | annobin: Generate global annotations
PLUGIN_ALL_PASSES_START          | annobin: Generate per-function annotations
PLUGIN_ALL_PASSES_END            | annobin: Register per-function end symbol
glue.c:1: internal compiler error: Segmentation fault
    1 | #define STRICT_R_HEADERS
      | 
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/cc6CRUqk.out file, please attach this to your bugreport.
make: *** [/usr/lib64/R/etc/Makeconf:167: glue.o] Error 1
ERROR: compilation failed for package ‘glue’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/glue’
ERROR: dependencies ‘digest’, ‘base64enc’, ‘rlang’ are not available for package ‘htmltools’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/htmltools’
ERROR: dependencies ‘Rcpp’, ‘rlang’ are not available for package ‘later’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/later’
ERROR: dependencies ‘Rcpp’, ‘later’, ‘rlang’ are not available for package ‘promises’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/promises’
ERROR: dependencies ‘Rcpp’, ‘promises’, ‘later’ are not available for package ‘httpuv’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/httpuv’
ERROR: dependencies ‘httpuv’, ‘mime’, ‘jsonlite’, ‘digest’, ‘htmltools’, ‘sourcetools’, ‘later’, ‘promises’, ‘rlang’, ‘fastmap’, ‘commonmark’, ‘glue’ are not available for package ‘shiny’
* removing ‘/home/daljit97/R/x86_64-redhat-linux-gnu-library/4.0/shiny’

The downloaded source packages are in
        ‘/tmp/RtmpztaPGd/downloaded_packages’
There were 15 warnings (use warnings() to see them)
标签： rshiny
r - 无法在 Fedora 上安装闪亮的 R 包

问题描述

解决方案

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