Question

我在过去几个小时内尝试使用以下输出安装 RMongo 包：

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我还发现了尝试安装 xlsx 的错误。

我不知道过去的发行版有什么变化，因为我已经尝试过使用Ubuntu 16.04.2和Ubuntu 17.04，结果相同。

这是Ubuntu 16.04.2发行版中R环境的描述：

> install.packages("RMongo")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://repo.bppt.go.id/cran/src/contrib/RMongo_0.0.25.tar.gz'
Content type 'application/x-gzip' length 4169519 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

* installing *source* package ‘RMongo’ ...
** package ‘RMongo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Segmentation fault (core dumped)
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/RMongo’

The downloaded source packages are in
    ‘/tmp/RtmpHZoomn/downloaded_packages’
Warning message:
In install.packages("RMongo") :
  installation of package ‘RMongo’ had non-zero exit status

有关可能发生的事情的任何想法吗？

Answer 1

linux-image-3.13.0-121-generic和linux-image-4.4.0-81-generic包含Stack Clash vulnerability的修复。

小心内核更新，修复此漏洞。当前的补丁打破了许多java（sun / oracle和openjdk）应用程序。见Bug #1699772: linux-image-4.4.0-81-generic, linux-image-3.13.0-121-generic Regression: many user-space apps crashing。解决方案是使用旧内核临时重启系统（在Trusty中为linux-image-3.13.0-119-generic）。

Ubuntu内核开发人员will prepare new patch in a few days。

更新：最新更新（至少图片-4.4.0-83-通用，linux-image-4.8.0-58-generic，linux-image-4.10.0-26-generic ）修复此漏洞和用户空间程序的问题。

Answer 2

这不能解决我在使用RMongo时遇到的问题，但解决了我的问题，所以我希望它有用。

我继续做一些测试。由于这个问题在RMongo突然停止工作时开始，并考虑到我有一个正常工作的类似安装，我开始比较两种环境。

我已经检查过，在失败的系统中，执行了一些软件更新（您可以在下面查看）：

The following NEW packages will be installed
  libmircommon7 libmircore1 linux-headers-4.4.0-81 linux-headers-4.4.0-81-generic linux-image-4.4.0-81-generic
  linux-image-extra-4.4.0-81-generic
The following packages will be upgraded:
  click firefox firefox-locale-en flashplugin-installer gir1.2-click-0.4 google-chrome-stable grub-common grub-pc
  grub-pc-bin grub2-common libc-bin libc-dev-bin libc6 libc6:i386 libc6-dbg libc6-dev libclick-0.4-0 libepoxy0
  libgnutls-openssl27 libgnutls30 libmirclient9 libmircookie2 libmirprotobuf3 libmwaw-0.3-3 libnss3 libnss3-nssdb
  libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5
  libqt5sql5-sqlite libqt5test5 libqt5widgets5 libqt5xml5 libssl-dev libssl-doc libssl1.0.0 libvlc5 libvlccore8
  libzzip-0-13 linux-firmware linux-headers-generic linux-image-generic linux-libc-dev locales multiarch-support
  openssl python3-click-package vlc vlc-data vlc-nox vlc-plugin-notify vlc-plugin-samba

所以，我已经逐一检查了这个包，结果发现问题的根源是新内核 4.4.0-81 。

为了确保这是问题的根源，我已经通过Ubuntu发行版启动了我在笔记本电脑中使用的以前版本的内核： 4.4.0-79

这是安装的结果：

> install.packages("RMongo")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/RMongo_0.0.25.tar.gz'
Content type 'application/x-gzip' length 4169519 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

* installing *source* package ‘RMongo’ ...
** package ‘RMongo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RMongo)

The downloaded source packages are in
    ‘/tmp/RtmpJScKfz/downloaded_packages’
> install.packages("xlsx")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/xlsx_0.5.7.tar.gz'
Content type 'application/x-gzip' length 312839 bytes (305 KB)
==================================================
downloaded 305 KB

* installing *source* package ‘xlsx’ ...
** package ‘xlsx’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xlsx)

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

这两个软件包 xlsx 和 RMongo 现已成功安装并正常运行。

我还检查了 xlsx 和 RMongo 之间的关系，我担心下面的问题是 rJava （常见的依赖关系）。事实上，为了确保这一点，我已经使用其他依赖rJava的包（ RWeka ）进行了测试，我遇到了同样的问题，在更改内核版本后解决了。< / p>

==更新==

在上次内核更新后，从4.4.0-81到4.4.0-83，问题已得到解决。

Answer 3

同样的问题（至少对于包“xlsx”）发生在内核3.13.0-121-generic的Ubuntu 14.04 LTS中。使用以前的内核（3.13.0-119-generic）启动时，安装工作和库加载。

更新：问题似乎在新内核3.13.0-123-generic

的Ubuntu 14.04 LTS中得到解决

在Ubuntu中，RMongo安装失败并出现Segmentation Fault

3 个答案: