安装包时的非零退出状态答案

【问题标题】：Non zero exit status when installing packages安装包时的非零退出状态
【发布时间】：2018-10-04 21:01:07
【问题描述】：

我正在尝试在 CentOs 托管的 RStudio 上安装软件包。最初控制台输出告诉我安装一些软件包，包括我使用 yum install 安装的 libcurl-devel 或 libxml2-devel。

我可以安装一些软件包。但是，tidyverse 给了我一些问题。尝试安装后我无法理解控制台输出，所以我将其粘贴在下面。谁能建议如何克服这个问题以便我可以安装 tidyverse？

install.packages("tidyverse", dependencies = T)
Installing package into ‘/home/rstudio/mylibs’
(as ‘lib’ is unspecified)
also installing the dependency ‘lubridate’

trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.4.tar.gz'
Content type 'application/x-gzip' length 449850 bytes (439 KB)
==================================================
downloaded 439 KB

trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.2.1.tar.gz'
Content type 'application/x-gzip' length 61647 bytes (60 KB)
==================================================
downloaded 60 KB

* installing *source* package ‘lubridate’ ...
** package ‘lubridate’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/rstudio/mylibs/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/rstudio/mylibs/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c datetime.c -o datetime.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/rstudio/mylibs/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c period.c -o period.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/rstudio/mylibs/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c tparse.c -o tparse.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I"/home/rstudio/mylibs/Rcpp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c update.cpp -o update.o
In file included from ./cctz/include/civil_time.h:18,
                 from update.cpp:4:
./cctz/include/civil_time_detail.h:37: error: expected nested-name-specifier before ‘year_t’
./cctz/include/civil_time_detail.h:37: error: ‘year_t’ has not been declared
./cctz/include/civil_time_detail.h:37: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:37: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:41: error: expected nested-name-specifier before ‘diff_t’
./cctz/include/civil_time_detail.h:41: error: ‘diff_t’ has not been declared
./cctz/include/civil_time_detail.h:41: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:41: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:46: error: expected nested-name-specifier before ‘month_t’
./cctz/include/civil_time_detail.h:46: error: ‘month_t’ has not been declared
./cctz/include/civil_time_detail.h:46: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:46: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:47: error: expected nested-name-specifier before ‘day_t’
./cctz/include/civil_time_detail.h:47: error: ‘day_t’ has not been declared
./cctz/include/civil_time_detail.h:47: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:47: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:48: error: expected nested-name-specifier before ‘hour_t’
./cctz/include/civil_time_detail.h:48: error: ‘hour_t’ has not been declared
./cctz/include/civil_time_detail.h:48: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:48: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:49: error: expected nested-name-specifier before ‘minute_t’
./cctz/include/civil_time_detail.h:49: error: ‘minute_t’ has not been declared
./cctz/include/civil_time_detail.h:49: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:49: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:50: error: expected nested-name-specifier before ‘second_t’
./cctz/include/civil_time_detail.h:50: error: ‘second_t’ has not been declared
./cctz/include/civil_time_detail.h:50: error: expected ‘;’ before ‘=’ token
./cctz/include/civil_time_detail.h:50: error: expected unqualified-id before ‘=’ token
./cctz/include/civil_time_detail.h:54: error: expected ‘)’ before ‘year’
./cctz/include/civil_time_detail.h:78: error: ‘cctz::detail::impl::is_leap_year’ declared as an ‘inline’ variable
./cctz/include/civil_time_detail.h:78: error: ‘year_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:78: error: expected ‘,’ or ‘;’ before ‘noexcept’
./cctz/include/civil_time_detail.h:81: error: ‘cctz::detail::impl::year_index’ declared as an ‘inline’ variable
./cctz/include/civil_time_detail.h:81: error: ‘year_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:81: error: ‘month_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:81: error: initializer expression list treated as compound expression
./cctz/include/civil_time_detail.h:81: error: expected ‘,’ or ‘;’ before ‘noexcept’
./cctz/include/civil_time_detail.h:84: error: ‘cctz::detail::impl::days_per_century’ declared as an ‘inline’ variable
./cctz/include/civil_time_detail.h:84: error: ‘year_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:84: error: ‘month_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:84: error: initializer expression list treated as compound expression
./cctz/include/civil_time_detail.h:84: error: expected ‘,’ or ‘;’ before ‘noexcept’
./cctz/include/civil_time_detail.h:88: error: ‘cctz::detail::impl::days_per_4years’ declared as an ‘inline’ variable
./cctz/include/civil_time_detail.h:88: error: ‘year_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:88: error: ‘month_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:88: error: initializer expression list treated as compound expression
./cctz/include/civil_time_detail.h:88: error: expected ‘,’ or ‘;’ before ‘noexcept’
./cctz/include/civil_time_detail.h:92: error: ‘cctz::detail::impl::days_per_year’ declared as an ‘inline’ variable
./cctz/include/civil_time_detail.h:92: error: ‘year_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:92: error: ‘month_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:92: error: initializer expression list treated as compound expression
./cctz/include/civil_time_detail.h:92: error: expected ‘,’ or ‘;’ before ‘noexcept’
./cctz/include/civil_time_detail.h:95: error: ‘cctz::detail::impl::days_per_month’ declared as an ‘inline’ variable
./cctz/include/civil_time_detail.h:95: error: ‘year_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:95: error: ‘month_t’ was not declared in this scope
./cctz/include/civil_time_detail.h:95: error: initializer expression list treated as compound expression
./cctz/include/civil_time_detail.h:95: error: expected ‘,’ or ‘;’ before ‘noexcept’
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/functional:56,
                 from /home/rstudio/mylibs/Rcpp/include/RcppCommon.h:61,
                 from /home/rstudio/mylibs/Rcpp/include/Rcpp.h:27,
                 from update.cpp:7:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/typeinfo:36: error: expected ‘}’ before end of line
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/typeinfo:36: error: expected ‘}’ before end of line
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/typeinfo:36: error: expected ‘}’ before end of line
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/typeinfo:36: error: expected declaration before end of line
make: *** [update.o] Error 1
ERROR: compilation failed for package ‘lubridate’
* removing ‘/home/rstudio/mylibs/lubridate’
Warning in install.packages :
  installation of package ‘lubridate’ had non-zero exit status
ERROR: dependency ‘lubridate’ is not available for package ‘tidyverse’
* removing ‘/home/rstudio/mylibs/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmp0Wx5ys/downloaded_packages’

【问题讨论】：

我会尝试卸载任何当前版本的lubridate，自行安装lubridate，然后尝试重新安装tidyverse。
感谢@C.Braun 的建议。我已经尝试了所有这些事情。 Lubridate 无法自行安装。我什至尝试通过 install_github 安装 lubridate（然后是 tidyverse），但这也失败了
如果 lubridate 无法自行安装，这似乎更像是该软件包的问题，而不是整个 tidyverse。
您需要通读this GitHub issue thread。其他人在 RHEL（CentOS 所基于的）上遇到了这个问题，这可能与过时的 gcc 有关。那里的一些人看起来已经解决了这个问题（通过安装旧版本的 lubridate），但也许其他人没有那么多（即使在更新 gcc 之后）。
我使用devtools::install_github("tidyverse/lubridate@before-CCTZ") 从该线程安装了旧版本的 lubridate。那是成功的。但是，在那之后我尝试安装 tidyverse，这给了我这个错误“loadNamespace 中的错误（j = 1.7.1 是必需的”。是否可以安装旧版本的 tidyverse，如果可以，我如何知道可以使用此版本的 lubridate 安装哪个版本？

标签： r tidyverse

【解决方案1】：

根据 cmets，这个问题似乎更多地与 CentOs6 相关，而不是 R 或 Tidyverse。我安装了旧版本的 lubridate，它似乎无法作为 tidyverse 软件包的一部分安装：

devtools::install_github("tidyverse/lubridate@before-CCTZ")

我在安装此旧版本的 lubridate 后尝试安装 tidyverse，但失败并显示类似的错误消息。

然后我安装了一个旧版本的 tidyverse，然后成功安装：

devtools::install_version("tidyverse", version = "1.1.1", repos = "http://cran.us.r-project.org")

【讨论】：