RMongo安装失败，分段故障在Ubuntu

我已经为过去的几个小时试图安装RMongo包以下的输出：RMongo安装失败，分段故障在Ubuntu

> 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

我也发现了同样的错误尝试安装xlsx。

我不知道在过去的发行版中发生了什么变化，因为我已经在Ubuntu 16.04.2和Ubuntu 17.04上试了这个，结果相同。

这是R环境在Ubuntu 16.04.2发行说明：

> sessionInfo() 
R version 3.4.0 (2017-04-21) 
Platform: x86_64-pc-linux-gnu (64-bit) 
Running under: Ubuntu 16.04.2 LTS 
Matrix products: default 
BLAS: /usr/lib/libblas/libblas.so.3.6.0 
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 
locale: 
[1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C    
[3] LC_TIME=es_ES.UTF-8  LC_COLLATE=en_US.UTF-8  
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=es_ES.UTF-8  LC_NAME=C     
[9] LC_ADDRESS=C    LC_TELEPHONE=C    
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C  
attached base packages: 
[1] stats  graphics grDevices utils  datasets methods base  
loaded via a namespace (and not attached): 
[1] compiler_3.4.0 tools_3.4.0 tcltk_3.4.0

什么可以发生任何想法？

来源

2017-06-21 asuka

这并没有回答我遇到的与RMongo相关的问题，但是为我解决了这个问题，所以我希望它能够有用。

我继续做一些测试。由于这个问题是在RMongo突然停止工作时开始的，考虑到我有一个类似的工作正常，我开始比较两种环境。

我检查了，因为出现故障，进行一些软件更新系统（你可以在下面检查它们）：

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，我通过一个本包检查之一，事实证明问题的根源在于新内核4.4.0-81。

为了确保这是问题的根源，我已经被Ubuntu发行版推出了与以前的版本，我曾在我的笔记本电脑的内核：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’

两种封装，XLSX和RMongo，现已成功安装并正常工作。

我还检查XLSX和RMongo之间的关系，恐怕这个问题下面是rJava（常见应用）。事实上，为了确保这一点，我已经用其他软件包rJava相关的（RWeka）进行了测试，并且我遇到了同样的问题，在更改内核版本后解决。

== == UPDATE

最后内核更新后，从4.4.0-81至4.4.0-83，该问题已得到修复。

来源

2017-06-22 12:27:51 asuka

同样的问题（至少对于软件包“xlsx”）发生在Ubuntu 14.04 LTS内核3.13.0-121-generic。使用以前的内核（3.13.0-119-generic）进行引导时，安装工作并加载库。

UPDATE：问题出现14.04 LTS的新内核3.13.0-123泛型

来源

2017-06-22 14:05:15

Debian和内核4.9.0-3-amd64在这里也是一样。 – vodka

的linux-image-3.13.0-121泛型和linux-图像4.4.0-81在Ubuntu要解决-generic包含Stack Clash vulnerability的修复程序。

请注意使用内核更新来修复此漏洞。当前的补丁破坏了许多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内核开发者will prepare new patch in a few days。

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

来源

2017-06-24 16:36:59 N0rbert

最后一次内核更新后，从4.4.0-81到4.4.0-83，问题已修复。 – asuka

RMongo安装失败，分段故障在Ubuntu

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