最开始是想安装 Bioconductor 中的 minfi（https://github.com/hansenlab/minfi） 这个 R 包，但是发现不管是 conda 还是 BiocManager::install(“minfi”) 总不能成功，依赖包贼多不说，有些依赖包还特别坑爹。

    首先要说的是 sparseMatrixStats（https://github.com/const-ae/sparseMatrixStats），虽然这个包比较坑，但作者起码在 GitHub 上给出了说明和解决方法。

    最坑的应该是一个叫 rhdf5filters（https://github.com/grimbough/rhdf5filters）的 R 包，费劲了九牛二虎之力都搞不定，尤其是在 GCC-4.8.5 编译器下有人说 “assume it is just obsolete compiler”，让我感觉到我的 CentOS-6.5 +gcc-4.8.5 想要安装好它基本是没戏了！
    image.png

    几经折腾，虽然最终在 R-3.4 中倒腾成功了，但是对于 R>=3.5 总是耿耿于怀想再尝试一下（不见棺材不落泪 😭😭😭），结合到前几天看到的 devtoolset，于是想着去折腾一下。

    有时候现实就是这么残酷，摩拳擦掌蠢蠢欲试，有时候结果会让你直接吐血——在安装 devtoolset 的时候总发现有这么一条重复出现且让人讨厌的 openssl 错误信息：

    :::warning ** Found 1 pre-existing rpmdb problem(s), ‘yum check’ output follows:
    openssl-1.0.1e-57.el6.x86_64 is a duplicate with openssl-1.0.1e-15.el6.x86_64 ::: image.png
    初生牛犊不怕虎（其实当时应该先谷歌一下能不能卸载 😳😳😳），也没想太多于是就把重复的 openssl-1.0.1e-57.el6.x86_64 卸载了！！！ :::warning $ rpm -e openssl-1.0.1e-57.el6.x86_64 ::: image.png
    接下来，惊魂的酸爽时刻来了：

    1. yum 不能用了，开始提示 libssl.so.10 不存在！ :::warning libssl.so.10: cannot open shared object file: No such file or directory :::

    2. 新的 Terminal 想要通过 SSH 再次登陆 log01，提示网络被关闭，登陆不上去了！！

    开始意识到出问题了，于是去谷歌，搜索完差点一口老血喷出来！但万幸的是 root 还没有退出来！！！

    于是开始自救！

    首先，下载对应版本的 rpm（这时候 wget/scp 都罢工了！），上传到服务器，然后 rpm 安装。

    最先下载的是 openssl-1.0.0-27.el6.src.rpm，但 rpm 安装的时候又出现了新的问题。

    1. [root@log01 lib64]# rpm -ivh /home/bioadmin/openssl-1.0.0-27.el6.src.rpm
    2. warning: /home/bioadmin/openssl-1.0.0-27.el6.src.rpm: Header V3 RSA/SHA256 Signature, key ID fd431d51: NOKEY
    3.    1:openssl                warning: user mockbuild does not exist - using root
    4. warning: group mockbuild does not exist - using root
    5. warning: user mockbuild does not exist - using root
    6. warning: group mockbuild does not exist - using root
    7. ......
    8. warning: group mockbuild does not exist - using root
    9. ########################################### [100%]
    10. warning: user mockbuild does not exist - using root
    11. warning: group mockbuild does not exist - using root
    12. warning: user mockbuild does not exist - using root
    13. warning: group mockbuild does not exist - using root
    15. [root@log01 lib64]# sudo useradd -s /sbin/nologin mockbuild
    16. [root@log01 lib64]# rpm -ivh /RiboBio/home/bi.chengnan/R/openssl-1.0.0-27.el6.src.rpm
    17. warning: /RiboBio/home/bi.chengnan/R/openssl-1.0.0-27.el6.src.rpm: Header V3 RSA/SHA256 Signature, key ID fd431d51: NOKEY
    18.    1:openssl                ########################################### [100%]

    安装完，发现不起作用，/usr/lib64 下面缺失的 libssl.so.10 和 libcrypto.so.10 没有回来，SSH 依然无法登陆。

    接着，下载卸载的 openssl-1.0.1e-57.el6.x86_64.rpm，不出意外 rpm 安装又遇到新的问题（心底一万个草泥马飘过）！

    1. [root@log01 usr]# rpm -ivh /home/bioadmin/openssl-1.0.1e-57.el6.x86_64.rpm
    2. warning: /home/bioadmin/openssl-1.0.1e-57.el6.x86_64.rpm: Header V3 RSA/SHA1 Signature, key ID c105b9de: NOKEY
    3. Preparing...                ########################################### [100%]
    4.         file /usr/bin/openssl from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    5.         file /usr/lib64/.libcrypto.so.1.0.1e.hmac from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    6.         file /usr/lib64/.libssl.so.1.0.1e.hmac from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    7.         file /usr/lib64/libcrypto.so.1.0.1e from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    8.         file /usr/lib64/libssl.so.1.0.1e from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    9.         file /usr/lib64/openssl/engines/lib4758cca.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    10.         file /usr/lib64/openssl/engines/libaep.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    11.         file /usr/lib64/openssl/engines/libatalla.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    12.         file /usr/lib64/openssl/engines/libcapi.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    13.         file /usr/lib64/openssl/engines/libchil.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    14.         file /usr/lib64/openssl/engines/libcswift.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    15.         file /usr/lib64/openssl/engines/libgmp.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    16.         file /usr/lib64/openssl/engines/libnuron.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    17.         file /usr/lib64/openssl/engines/libpadlock.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    18.         file /usr/lib64/openssl/engines/libsureware.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    19.         file /usr/lib64/openssl/engines/libubsec.so from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    20.         file /usr/share/doc/openssl-1.0.1e/README.FIPS from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    21.         file /usr/share/man/man1/ca.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    22.         file /usr/share/man/man1/ciphers.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    23.         file /usr/share/man/man1/cms.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    24.         file /usr/share/man/man1/ec.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    25.         file /usr/share/man/man1/ocsp.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    26.         file /usr/share/man/man1/openssl.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    27.         file /usr/share/man/man1/req.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    28.         file /usr/share/man/man1/s_client.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    29.         file /usr/share/man/man1/s_server.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    30.         file /usr/share/man/man1/s_time.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    31.         file /usr/share/man/man1/smime.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    32.         file /usr/share/man/man1/speed.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    33.         file /usr/share/man/man1/ts.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    34.         file /usr/share/man/man1/verify.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    35.         file /usr/share/man/man1/x509.1ssl.gz from install of openssl-1.0.1e-57.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64

    第三，尝试 openssl-1.0.1e-15.el6.x86_64.rpm，居然还是这个问题（。。。。。）！

    1. [root@log01 usr]# rpm -ivh /home/bioadmin/openssl-1.0.1e-15.el6.x86_64.rpm
    2. warning: /home/bioadmin/R/openssl-1.0.1e-15.el6.x86_64.rpm: Header V3 RSA/SHA1 Signature, key ID c105b9de: NOKEY
    3. Preparing...                ########################################### [100%]
    4.         package openssl-1.0.1e-15.el6.x86_64 is already installed
    5.         file /usr/bin/openssl from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    6.         file /usr/lib64/.libcrypto.so.1.0.1e.hmac from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    7.         file /usr/lib64/.libssl.so.1.0.1e.hmac from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    8.         file /usr/lib64/libcrypto.so.1.0.1e from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    9.         file /usr/lib64/libssl.so.1.0.1e from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    10.         file /usr/lib64/openssl/engines/lib4758cca.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    11.         file /usr/lib64/openssl/engines/libaep.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    12.         file /usr/lib64/openssl/engines/libatalla.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    13.         file /usr/lib64/openssl/engines/libcapi.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    14.         file /usr/lib64/openssl/engines/libchil.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    15.         file /usr/lib64/openssl/engines/libcswift.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    16.         file /usr/lib64/openssl/engines/libgmp.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    17.         file /usr/lib64/openssl/engines/libnuron.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    18.         file /usr/lib64/openssl/engines/libpadlock.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    19.         file /usr/lib64/openssl/engines/libsureware.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    20.         file /usr/lib64/openssl/engines/libubsec.so from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    21.         file /usr/share/man/man1/ca.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    22.         file /usr/share/man/man1/cms.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    23.         file /usr/share/man/man1/ec.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    24.         file /usr/share/man/man1/ocsp.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    25.         file /usr/share/man/man1/openssl.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    26.         file /usr/share/man/man1/req.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    27.         file /usr/share/man/man1/s_client.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    28.         file /usr/share/man/man1/s_server.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    29.         file /usr/share/man/man1/s_time.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    30.         file /usr/share/man/man1/smime.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    31.         file /usr/share/man/man1/ts.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    32.         file /usr/share/man/man1/verify.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64
    33.         file /usr/share/man/man1/x509.1ssl.gz from install of openssl-1.0.1e-15.el6.x86_64 conflicts with file from package openssl-1.0.1e-15.el6.x86_64

    第四，尝试下载 openssl-1.0.1e.tar.gz 源码包安装，但是 make 的时候却出现了 Perl 有关的 Error（注意这里是一个很关键的步骤），最开始也以为要凉凉了！！

    虽然在《Centos6 卸载 OpenSSL 后重装提示 libssl.so.10: cannot open shared object file: No such file or directory》这篇文章中提到：”Make：通过 make 来生成生成libssl.so.1.0.0 和 libcrypto.so.1.0.0“，对这句话一直不理解以为是要安装完成后，在目标目录才会生成 libssl.so.1.0.0 和 libcrypto.so.1.0.0！其实并非如此！

    1. $ tar zvxf openssl-1.0.1e.tar.gz
    2. $ cd openssl-1.0.1e
    3. $ ./config shared zlib-dynamic
    4. $ make
    5. ......
    6. installing man1/asn1parse.1
    7. installing man1/CA.pl.1
    8. installing man1/ca.1
    9. installing man1/ciphers.1
    10. installing man1/cms.1
    11. cms.pod around line 457: Expected text after =item, not a number
    12. cms.pod around line 461: Expected text after =item, not a number
    13. cms.pod around line 465: Expected text after =item, not a number
    14. cms.pod around line 470: Expected text after =item, not a number
    15. cms.pod around line 474: Expected text after =item, not a number
    16. POD document had syntax errors at /RiboBio/Bioinfo/APPS/perl/bin/pod2man line 71.
    17. make: *** [install_docs] Error 1

    其实，make 这一步已经在当前目录（注意是当前执行编译的目录）生成我们想要的 libssl.so.1.0.0 和 libcrypto.so.1.0.0 了！！！
    image.png
    第五，把这两个文件 ln -s 到 /usr/lib64，神奇的发现 yum 居然恢复正常了，虽然 SSH 还是不能登录。

    1. [root@log01 lib64]# ln -s /home/bioadmin/src/openssl-1.0.1e/libssl.so.1.0.0 /usr/lib64/libssl.so.10
    2. [root@log01 lib64]# ln -s /home/bioadmin/src/openssl-1.0.1e/libcrypto.so.1.0.0 /usr/lib64/libcrypto.so.10

    image.png

    最后，尝试着使用 yum 把 openssl 重新安装一下。这一次发现，一切都恢复正常了！
    image.png

    参考资料：

    1. 程序员宅基地，《Centos6 卸载 OpenSSL 后重装提示 libssl.so.10: cannot open shared object file: No such file or directory》，程序员宝宝
    2. augusite，《libssl.so.10: cannot open shared object file: No such file or directory - augusite - 博客园》
    3. OpenSSL tar.gz 源码包下载地址：Index of /source/old/1.0.1
    4. OpenSSL rpm 源码下载地址：https://mirrors.aliyun.com/centos-vault/6.5/updates/x86_64/Packages/