最近看到引力波相關內容，其中關於科學家們使用了一個python的第三方包：GWPY包。好奇之下，自己也安裝了一下這個python包。但是發現一個問題。Mac系統自帶的python無法更新第三方包，其中報錯的是numpy包，錯誤如下：

Collecting numpy

Using cached numpy-1.10.2-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whlInstalling
 collected packages: numpy
 Found existing installation: numpy 1.8
 
.0rc1
 DEPRECATION: Uninstalling a distutils installed project (numpy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
 Uninstalling numpy-1.8.0rc1:Exception:Traceback
 (most recent call last
 
):
 File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/basecommand.py", line 211, in main
 status = self.run(options, args)
 File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/commands/install.py", line 311, in run
 root=options.root_path,
 File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_set.py"
 
, line 640, in install
 requirement.uninstall(auto_confirm=True)
 File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_install.py", line 716, in uninstall
 paths_to_remove.remove(auto_confirm)
 File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/req/req_uninstall.py", line 125, in remove
 renames(path, new_path)
 File "/Library/Python/2.7/site-packages/pip-7.1.2-py2.7.egg/pip/utils/__init__.py",
 line 315, in renames
shutil.move(old, new)
 File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 302, in move
 copy2(src, real_dst)
 File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 131, in copy2
 copystat(src, dst)
 File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 103, in copystat
 os.chflags(dst, st.st_flags)OSError:
 [Errno 1] Operation not permitted: '/var/folders/5n/vbm997m56xg3kw67y6bccn2m0000gn/T/pip-4tcBsd-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info'

使用pip 重新安裝 numpy 包

pip install -U numpy

依然報錯，錯誤輸出的內容和上面的一致。

冷靜下來後重新看了一些錯，Operation not permitted 沒有操作許可權。奇怪了，系統在10.9和10.10的時候都沒有出現這種情況，難道是蘋果自己搞的鬼？

自己無法解決，只好求助於“度娘“ 和谷歌，不懈努力後還真的發現了問題。

經歷了XCode編譯器程式碼被注入的事件後，這次 Mac OS X El Capitan系統的升級，啟用了更高的安全性保護機制：系統完整性保護System Integrity Protection (SIP)。簡單來講就是更加強制性的保護系統相關的資料夾。開發者不能直接操作相關的檔案內容。

蘋果官方的解釋
System Integrity Protection is a security technology in OS X El Capitan that’s designed to help prevent potentially malicious software from modifying protected files and folders on your Mac.
In OS X, the “root” user account previously had no permission restrictions and could access any system folder or application on your Mac. Software gained root-level access when you entered your administrator name and password to install it and could then modify or overwrite any system file or application.
System Integrity Protection restricts the root account and limits the actions that the root user can perform on protected parts of OS X.
Paths and applications protected by System Integrity Protection include:
/System
/usr
/bin
/sbin
Apps that are pre-installed with OS X
Paths and applications that third-party apps and installers can write to include:
/Applications
/Library
/usr/local
System Integrity Protection is designed to allow modifications of these protected parts only by processes that are signed by Apple and have special entitlements to write to system files, like Apple software updates and Apple installers.
Apps that you download from the Mac App Store already work with System Integrity Protection. Other third-party software that conflicts with System Integrity Protection might be set aside when you upgrade to OS X El Capitan.
System Integrity Protection also helps prevent software from changing your startup volume. To boot your Mac from a different volume, you can use the Startup Disk pane in System Preferences or you can hold down the Option key while you reboot, and select a volume from the list.
Information about products not manufactured by Apple, or independent websites not controlled or tested by Apple, is provided without recommendation or endorsement. Apple assumes no responsibility with regard to the selection, performance, or use of third-party websites or products. Apple makes no representations regarding third-party website accuracy or reliability. Risks are inherent in the use of the Internet. Contact the vendor for additional information. Other company and product names may be trademarks of their respective owners.
Last Modified: Oct 2, 2015
來源： https://support.apple.com/en-us/HT204899

找到問題的原因就可以解決相關的問題了，解決問題的方法就是關閉Mac系統的“SIP“。

具體的操作步驟，引用國外的一個牛人給出的方法：
How to turn off System Integrity Protection in El Capitan

1. Click the  menu.
2. Select Restart…
3. Hold down command-R to boot into the Recovery System.
4. Click the Utilities menu and select Terminal.
5. Type csrutil disable and press return .
6. Close the Terminal app.
7. Click the  menu and select Restart… .

好吧，照顧一下看不懂英語的朋友。

1. 點選Mac電腦的蘋果圖示
2. 選擇 重新啟動
3. 按住 command＋R，直到進入還原模式
4. 選擇實用工具，然後點選 終端
5. 輸入 csrutil disable 按下回車
6. 重啟電腦

這樣就將“SIP“關閉了。

然後我們使用 pip 安裝升級numpy、scipy等相關的包。

問題是解決了，但是如果到這裡就認為已經萬事大吉了，其實是大錯特錯了。蘋果官方之所以設定“SIP“主要是考慮到系統的安全性問題。所以，我們最好還是將“SIP“開啟。開啟的方式如下：
1. 點選Mac電腦的蘋果圖示
2. 選擇 重新啟動
3. 按住 command＋R，直到進入還原模式
4. 選擇實用工具，然後點選 終端
5. 輸入 csrutil enable 按下回車
6. 重啟電腦

萬事大吉，收工睡覺！