error deploying scrapyd project - scrapy

when trying to execute this command:
scrapyd-deploy test -p project=myProject
I get the following error:
Traceback (most recent call last):
File "/usr/bin/scrapyd-deploy", line 269, in <module>
main()
File "/usr/bin/scrapyd-deploy", line 95, in main
egg, tmpdir = _build_egg()
File "/usr/bin/scrapyd-deploy", line 236, in _build_egg
retry_on_eintr(check_call, [sys.executable, 'setup.py', 'clean', '-a', 'bdist_egg', '-d', d], stdout=o, stderr=e)
File "/usr/local/lib/python2.7/dist-packages/scrapy/utils/python.py", line 331, in retry_on_eintr
return function(*args, **kw)
File "/usr/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/bin/python', 'setup.py', 'clean', '-a', 'bdist_egg', '-d', '/tmp/scrapydeploy-wV3h4k']' returned non-zero exit status 1
I have installed scrapyd-deploy and scrapyd-client, as well as setuptools and scrapyd of course.
This command:
python setup.py clean -a bdist_egg
produces the output:
running clean
removing 'build/lib.linux-x86_64-2.7' (and everything under it)
removing 'build/bdist.linux-x86_64' (and everything under it)
'build/scripts-2.7' does not exist -- can't clean it
removing 'build'
running bdist_egg
running egg_info
writing NOAA.egg-info/PKG-INFO
writing top-level names to NOAA.egg-info/top_level.txt
writing dependency_links to NOAA.egg-info/dependency_links.txt
writing entry points to NOAA.egg-info/entry_points.txt
reading manifest file 'NOAA.egg-info/SOURCES.txt'
writing manifest file 'NOAA.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/NOAA
copying NOAA/pipelines.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/__init__.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/noaa-template.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/noaa-original.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/settings-template.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/tika-python.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/settings.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/mysqldb.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/noaa.py -> build/lib.linux-x86_64-2.7/NOAA
copying NOAA/items.py -> build/lib.linux-x86_64-2.7/NOAA
creating build/lib.linux-x86_64-2.7/NOAA/spiders
copying NOAA/spiders/spider1.py -> build/lib.linux-x86_64-2.7/NOAA/spiders
copying NOAA/spiders/spider2.py -> build/lib.linux-x86_64-2.7/NOAA/spiders
(output omitted... There are a lot of spiders)
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/NOAA
copying build/lib.linux-x86_64-2.7/NOAA/pipelines.py -> build/bdist.linux-x86_64/egg/NOAA
creating build/bdist.linux-x86_64/egg/NOAA/spiders
copying build/lib.linux-x86_64-2.7/NOAA/spiders/spider1.py -> build/bdist.linux-x86_64/egg/NOAA/spiders
copying build/lib.linux-x86_64-2.7/NOAA/spiders/spider2.py -> build/bdist.linux-x86_64/egg/NOAA/spiders
(output omitted... There are a lot of spiders)
byte-compiling build/bdist.linux-x86_64/egg/NOAA/pipelines.py to pipelines.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/spiders/spider1.py to spider1.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/spiders/spider2.py to spider2.pyc
(output omitted... There are a lot of spiders)
byte-compiling build/bdist.linux-x86_64/egg/NOAA/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/noaa-template.py to noaa-template.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/noaa-original.py to noaa-original.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/settings-template.py to settings-template.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/tika-python.py to tika-python.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/settings.py to settings.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/mysqldb.py to mysqldb.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/noaa.py to noaa.pyc
byte-compiling build/bdist.linux-x86_64/egg/NOAA/items.py to items.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying NOAA.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying NOAA.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying NOAA.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying NOAA.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying NOAA.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/NOAA-1.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
When trying to schedule a spider with this command:
curl http://localhost:6800/schedule.json -d project=myproject -d spider=spider1.py
I get this error:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/twisted/web
req.requestReceived(command, path, version)
File "/usr/local/lib/python2.7/dist-packages/twisted/web
self.process()
File "/usr/local/lib/python2.7/dist-packages/twisted/web
self.render(resrc)
File "/usr/local/lib/python2.7/dist-packages/twisted/web
body = resrc.render(self)
--- <exception caught here> ---
File "/usr/local/lib/python2.7/dist-packages/scrapyd/web
return JsonResource.render(self, txrequest)
File "/usr/local/lib/python2.7/dist-packages/scrapyd/uti
r = resource.Resource.render(self, txrequest)
File "/usr/local/lib/python2.7/dist-packages/twisted/web
return m(request)
File "/usr/local/lib/python2.7/dist-packages/scrapyd/web
spiders = get_spider_list(project)
File "/usr/local/lib/python2.7/dist-packages/scrapyd/uti
runner = Config().get('runner')
File "/usr/local/lib/python2.7/dist-packages/scrapyd/con
self.cp.read(sources)
File "/usr/lib/python2.7/ConfigParser.py", line 305, in
self._read(fp, filename)
File "/usr/lib/python2.7/ConfigParser.py", line 512, in
raise MissingSectionHeaderError(fpname, lineno, line)
ConfigParser.MissingSectionHeaderError: File contains no s
file: /etc/scrapyd/conf.d/twistd.pid, line: 1
'24262'
Funny thing is, if I add what I believe to be a section header ([section header])to that twistd.pid file, I get an error saying that it contains something other than a numerical value of the pid of twistd.
Are these issues interrelated?

I was getting the same error .. what worked for me was using the command with sudo.
The error might be because the command is not getting the proper permissions.
sudo scrapyd-deploy test -p project=myProject

Related

Problem with building Chromium for Windows on Mac host

I am trying to cross build chromium on mac host. I have followed the instructions from https://chromium.googlesource.com/chromium/src.git/+/HEAD/docs/win_cross.md and everything seems fine. But when I run autoninja -C out/win chrome I face with the following error. Any help would be appreciated.
ninja: Entering directory `out/win'
[0/1] Regenerating ninja files
ERROR at //build/config/win/visual_studio_version.gni:27:7: Script returned non-zero exit code.
exec_script("../../vs_toolchain.py", [ "get_toolchain_dir" ], "scope")
^----------
Current dir: /chromium/src/out/win/
Command: python3 /chromium/src/build/vs_toolchain.py get_toolchain_dir
Returned 1.
stderr:
Traceback (most recent call last):
File "/chromium/src/build/vs_toolchain.py", line 587, in <module>
sys.exit(main())
File "/chromium/src/build/vs_toolchain.py", line 583, in main
return commands[sys.argv[1]](*sys.argv[2:])
File "/chromium/src/build/vs_toolchain.py", line 561, in GetToolchainDir
win_sdk_dir = SetEnvironmentAndGetSDKDir()
File "/chromium/src/build/vs_toolchain.py", line 554, in SetEnvironmentAndGetSDKDir
return NormalizePath(os.environ['WINDOWSSDKDIR'])
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 679, in __getitem__
raise KeyError(key) from None
KeyError: 'WINDOWSSDKDIR'
See //third_party/angle/gni/angle.gni:35:5: whence it was imported.
import("//build/config/win/visual_studio_version.gni")
^----------------------------------------------------
See //chrome/elevation_service/BUILD.gn:7:1: whence it was imported.
import("//build/toolchain/win/midl.gni")
^--------------------------------------
See //BUILD.gn:660:7: which caused the file to be included.
"//chrome/elevation_service:elevation_service_unittests",
^-------------------------------------------------------
FAILED: build.ninja
../../buildtools/mac/gn --root=../.. -q --ide=vs --regeneration gen .
ninja: error: rebuilding 'build.ninja': subcommand failed

ModuleNotFoundError: No module named 'elmoformanylangs' when I installed ELMo in Colab

I followed the following steps to install ELMoForManyLangs
! git clone https://github.com/HIT-SCIR/ELMoForManyLangs.git
cd ELMoForManyLangs/
! python setup.py install
from elmoformanylangs import Embedder
ModuleNotFoundError Traceback (most recent call last)
in ()
----> 1 from elmoformanylangs import Embedder
2 # e = Embedder('./zhs.model/')
But I did successfully deployed it.
running install
running bdist_egg
running egg_info
creating elmoformanylangs.egg-info
writing elmoformanylangs.egg-info/PKG-INFO
writing dependency_links to elmoformanylangs.egg-info/dependency_links.txt
writing requirements to elmoformanylangs.egg-info/requires.txt
writing top-level names to elmoformanylangs.egg-info/top_level.txt
writing manifest file 'elmoformanylangs.egg-info/SOURCES.txt'
writing manifest file 'elmoformanylangs.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/elmoformanylangs
copying elmoformanylangs/biLM.py -> build/lib/elmoformanylangs
copying elmoformanylangs/__init__.py -> build/lib/elmoformanylangs
copying elmoformanylangs/__main__.py -> build/lib/elmoformanylangs
copying elmoformanylangs/utils.py -> build/lib/elmoformanylangs
copying elmoformanylangs/elmo.py -> build/lib/elmoformanylangs
copying elmoformanylangs/dataloader.py -> build/lib/elmoformanylangs
copying elmoformanylangs/frontend.py -> build/lib/elmoformanylangs
creating build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/lstm_cell_with_projection.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/encoder_base.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/embedding_layer.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/lstm.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/__init__.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/util.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/classify_layer.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/token_embedder.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/elmo.py -> build/lib/elmoformanylangs/modules
copying elmoformanylangs/modules/highway.py -> build/lib/elmoformanylangs/modules
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/elmoformanylangs
copying build/lib/elmoformanylangs/biLM.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
copying build/lib/elmoformanylangs/__init__.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
copying build/lib/elmoformanylangs/__main__.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
copying build/lib/elmoformanylangs/utils.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
copying build/lib/elmoformanylangs/elmo.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
creating build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/lstm_cell_with_projection.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/encoder_base.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/embedding_layer.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/lstm.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/__init__.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/util.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/classify_layer.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/token_embedder.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/elmo.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/modules/highway.py -> build/bdist.linux-x86_64/egg/elmoformanylangs/modules
copying build/lib/elmoformanylangs/dataloader.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
copying build/lib/elmoformanylangs/frontend.py -> build/bdist.linux-x86_64/egg/elmoformanylangs
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/biLM.py to biLM.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/__main__.py to __main__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/elmo.py to elmo.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/lstm_cell_with_projection.py to lstm_cell_with_projection.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/encoder_base.py to encoder_base.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/embedding_layer.py to embedding_layer.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/lstm.py to lstm.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/util.py to util.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/classify_layer.py to classify_layer.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/token_embedder.py to token_embedder.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/elmo.py to elmo.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/modules/highway.py to highway.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/dataloader.py to dataloader.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/elmoformanylangs/frontend.py to frontend.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying elmoformanylangs.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying elmoformanylangs.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying elmoformanylangs.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying elmoformanylangs.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying elmoformanylangs.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/elmoformanylangs-0.0.2-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing elmoformanylangs-0.0.2-py3.6.egg
Copying elmoformanylangs-0.0.2-py3.6.egg to /usr/local/lib/python3.6/dist-packages
Adding elmoformanylangs 0.0.2 to easy-install.pth file
Installed /usr/local/lib/python3.6/dist-packages/elmoformanylangs-0.0.2-py3.6.egg
Processing dependencies for elmoformanylangs==0.0.2
Searching for overrides
Reading https://pypi.org/simple/overrides/
Downloading https://files.pythonhosted.org/packages/7a/b2/2cb6a3fc8ee1dc8617e07e476be19723748ddfcce0c6b9db7a5f2d5b9598/overrides-2.0.tar.gz#sha256=63293d9b03629507396ddd961bd5773f136d602f34b9b3da93351dfa163fc0d9
Best match: overrides 2.0
Processing overrides-2.0.tar.gz
Writing /tmp/easy_install-_c47zox2/overrides-2.0/setup.cfg
Running overrides-2.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-_c47zox2/overrides-2.0/egg-dist-tmp-677wh9fn
zip_safe flag not set; analyzing archive contents...
Moving overrides-2.0-py3.6.egg to /usr/local/lib/python3.6/dist-packages
Adding overrides 2.0 to easy-install.pth file
Installed /usr/local/lib/python3.6/dist-packages/overrides-2.0-py3.6.egg
Searching for numpy==1.17.2
Best match: numpy 1.17.2
Adding numpy 1.17.2 to easy-install.pth file
Installing f2py script to /usr/local/bin
Installing f2py3 script to /usr/local/bin
Installing f2py3.6 script to /usr/local/bin
Using /tensorflow-2.0.0-rc2/python3.6
Searching for h5py==2.10.0
Best match: h5py 2.10.0
Adding h5py 2.10.0 to easy-install.pth file
Using /tensorflow-2.0.0-rc2/python3.6
Searching for torch==1.2.0
Best match: torch 1.2.0
Adding torch 1.2.0 to easy-install.pth file
Installing convert-caffe2-to-onnx script to /usr/local/bin
Installing convert-onnx-to-caffe2 script to /usr/local/bin
Using /usr/local/lib/python3.6/dist-packages
Searching for six==1.12.0
Best match: six 1.12.0
Adding six 1.12.0 to easy-install.pth file
Using /usr/local/lib/python3.6/dist-packages
Finished processing dependencies for elmoformanylangs==0.0.2
The path in e = Embedder('./zhs.model/') is the absolute path, it is not the relative path.
e.g. '/content/drive/Colab Notebooks/../zhs.model/'

Unable to setup WebRTC native android code on ubuntu instance

Followed steps provided in this web page https://webrtc.org/native-code/android/
When I executed command "ninja -C out/Debug AppRTCMobile" I got following response
ninja: Entering directory `out/Debug'
ninja: fatal: chdir to 'out/Debug' - No such file or directory
I got stuck here and need help to continue in executing the next steps to complete the code setup.
Ubuntu version - 16.04.2
I have followed the same procedure once again to setup the code. This time I got a new error
Steps:
-> fetch --nohooks webrtc_android
-> gclient sync
-> gn gen out/Debug --args='target_os="android" target_cpu="arm"'
-> ninja -C out/Debug
ninja: Entering directory `out/Debug'
[1/8508] ACTION
//base:android_runtime_jni_headers__jni_Runtime(//build/toolchain/android:android_clang_arm)
FAILED: gen/android_runtime_jni_headers/base/jni/Runtime_jni.h python
../../base/android/jni_generator/jni_generator.py --depfile
gen/base/android_runtime_jni_headers__jni_Runtime.d --jar_file
../../third_party/android_tools/sdk/platforms/android-26/android.jar
--input_file java/lang/Runtime.class --ptr_type=long --output_dir gen/android_runtime_jni_headers/base/jni --includes
../../../../../../base/android/jni_generator/jni_generator_helper.h
--native_exports_optional
Traceback (most recent call last):
File "../../base/android/jni_generator/jni_generator.py", line 1428,
in
sys.exit(main(sys.argv))
File "../../base/android/jni_generator/jni_generator.py", line 1421,
in main
GenerateJNIHeader(input_file, output_file, options) File "../../base/android/jni_generator/jni_generator.py", line 1326, in
GenerateJNIHeader
jni_from_javap = JNIFromJavaP.CreateFromClass(input_file, options)
File "../../base/android/jni_generator/jni_generator.py", line 662,
in CreateFromClass
stderr=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in
_execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
[3/8508] CC obj/third_party/boringssl/boringssl/v3_ncons.o
ninja: build stopped: subcommand failed.
Someone please help me in resolving this issue.
You have to generate the projects using GN before trying to compile. You have the instructions here:
https://webrtc.org/native-code/android/

Installing Pillow in Python 3.4, how do I get past this error?

So, I was trying to install PyAutoGui, when I got an error. I found that Pillow is the problem. I get an error when installing, how do I resolve this and successfully install Pillow? When executing in a cmd:
C:\Python34\Scripts\pip install Pillow
I receive the following log:
copying PIL\IcnsImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\IcoImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\Image.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageChops.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageCms.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageColor.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageDraw.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageDraw2.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageEnhance.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageFile.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageFilter.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageFont.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageGrab.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageMath.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageMode.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageMorph.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageOps.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImagePalette.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImagePath.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageQt.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageSequence.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageShow.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageStat.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageTk.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageTransform.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImageWin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\ImtImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\IptcImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\Jpeg2KImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\JpegImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\JpegPresets.py -> build\lib.win-amd64-3.4\PIL
copying PIL\McIdasImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\MicImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\MpegImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\MpoImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\MspImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\OleFileIO.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PaletteFile.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PalmImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PcdImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PcfFontFile.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PcxImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PdfImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PixarImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PngImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PpmImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PsdImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PSDraw.py -> build\lib.win-amd64-3.4\PIL
copying PIL\PyAccess.py -> build\lib.win-amd64-3.4\PIL
copying PIL\SgiImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\SpiderImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\SunImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\TarIO.py -> build\lib.win-amd64-3.4\PIL
copying PIL\TgaImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\TiffImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\TiffTags.py -> build\lib.win-amd64-3.4\PIL
copying PIL\WalImageFile.py -> build\lib.win-amd64-3.4\PIL
copying PIL\WebPImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\WmfImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\XbmImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\XpmImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\XVThumbImagePlugin.py -> build\lib.win-amd64-3.4\PIL
copying PIL\_binary.py -> build\lib.win-amd64-3.4\PIL
copying PIL\_tkinter_finder.py -> build\lib.win-amd64-3.4\PIL
copying PIL\_util.py -> build\lib.win-amd64-3.4\PIL
copying PIL\__init__.py -> build\lib.win-amd64-3.4\PIL
running egg_info
writing top-level names to Pillow.egg-info\top_level.txt
writing requirements to Pillow.egg-info\requires.txt
writing dependency_links to Pillow.egg-info\dependency_links.txt
writing Pillow.egg-info\PKG-INFO
warning: manifest_maker: standard file '-c' not found
reading manifest file 'Pillow.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.sh'
no previously-included directories found matching 'docs\_static'
warning: no previously-included files found matching '.coveragerc'
warning: no previously-included files found matching '.editorconfig'
warning: no previously-included files found matching '.landscape.yaml'
warning: no previously-included files found matching 'appveyor.yml'
warning: no previously-included files found matching 'build_children.sh'
warning: no previously-included files found matching 'tox.ini'
warning: no previously-included files matching '.git*' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.so' found anywhere in distribution
writing manifest file 'Pillow.egg-info\SOURCES.txt'
running build_ext
The headers or library files could not be found for zlib,
a required dependency when compiling Pillow from source.
Please see the install instructions at:
http://pillow.readthedocs.io/en/latest/installation.html
Traceback (most recent call last):
File "C:\Users\User\AppData\Local\Temp\pip_build_User\Pillow\setup.py", line 779, in <module>
zip_safe=not debug_build(), )
File "C:\Python34\lib\distutils\core.py", line 148, in setup
dist.run_commands()
File "C:\Python34\lib\distutils\dist.py", line 955, in run_commands
self.run_command(cmd)
File "C:\Python34\lib\distutils\dist.py", line 974, in run_command
cmd_obj.run()
File "C:\Python34\lib\site-packages\setuptools\command\install.py", line 54, in run
return _install.run(self)
File "C:\Python34\lib\distutils\command\install.py", line 554, in run
self.run_command('build')
File "C:\Python34\lib\distutils\cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "C:\Python34\lib\distutils\dist.py", line 974, in run_command
cmd_obj.run()
File "C:\Python34\lib\distutils\command\build.py", line 126, in run
self.run_command(cmd_name)
File "C:\Python34\lib\distutils\cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "C:\Python34\lib\distutils\dist.py", line 974, in run_command
cmd_obj.run()
File "C:\Python34\lib\distutils\command\build_ext.py", line 348, in run
self.build_extensions()
File "C:\Users\User\AppData\Local\Temp\pip_build_User\Pillow\setup.py", line 549, in build_extensions
raise RequiredDependencyException(f)
__main__.RequiredDependencyException: zlib
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\User\AppData\Local\Temp\pip_build_User\Pillow\setup.py", line 791, in <module>
raise RequiredDependencyException(msg)
__main__.RequiredDependencyException:
The headers or library files could not be found for zlib,
a required dependency when compiling Pillow from source.
Please see the install instructions at:
http://pillow.readthedocs.io/en/latest/installation.html
----------------------------------------
Cleaning up...
Command C:\Python34\python.exe -c "import setuptools, tokenize;__file__='C:\\Users\\User\\AppData\\Local\\Temp\\pip_build_User\\Pillow\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\User\AppData\Local\Temp\pip-r710478a-record\install-record.txt --single-version-externally-managed --compile failed with error code 1 in C:\Users\User\AppData\Local\Temp\pip_build_User\Pillow
Storing debug log for failure in C:\Users\User\pip\pip.log
C:\Users\User>
Just reinstalled everything. Works now.

Error with pip install biom-format 'numpy/arrayobject.h' file not found

I can't manage to install biom format using pip install biom-format.
This is the error I get.
N85566:~ smitra$ pip install biom-format
Collecting biom-format
Using cached biom-format-2.1.5.tar.gz
Requirement already satisfied (use --upgrade to upgrade): click in /usr/local/lib/python2.7/site-packages (from biom-format)
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.3.0 in /Library/Python/2.7/site-packages (from biom-format)
Requirement already satisfied (use --upgrade to upgrade): future>=0.14.3 in /usr/local/lib/python2.7/site-packages (from biom-format)
Collecting scipy>=0.13.0 (from biom-format)
Using cached scipy-0.17.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pyqi (from biom-format)
Building wheels for collected packages: biom-format
Running setup.py bdist_wheel for biom-format ... error
Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/w0/sg297rxj3738tghvhq3fhr5c0000gp/T/pip-build-TljllL/biom-format/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/w0/sg297rxj3738tghvhq3fhr5c0000gp/T/tmpmTturCpip-wheel- --python-tag cp27:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.10-x86_64-2.7
creating build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/err.py -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/exception.py -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/parse.py -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/table.py -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/util.py -> build/lib.macosx-10.10-x86_64-2.7/biom
creating build/lib.macosx-10.10-x86_64-2.7/tests
copying tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/tests
copying tests/test_err.py -> build/lib.macosx-10.10-x86_64-2.7/tests
copying tests/test_parse.py -> build/lib.macosx-10.10-x86_64-2.7/tests
copying tests/test_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests
copying tests/test_util.py -> build/lib.macosx-10.10-x86_64-2.7/tests
creating build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/installation_informer.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/metadata_adder.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/table_converter.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/table_head.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/table_normalizer.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/table_subsetter.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/table_summarizer.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/table_validator.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/uc_processor.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
copying biom/cli/util.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
creating build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_add_metadata.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_show_install_info.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_subset_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_summarize_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_table_converter.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_table_normalizer.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_uc_processor.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
copying tests/test_cli/test_validate_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
running egg_info
writing requirements to biom_format.egg-info/requires.txt
writing biom_format.egg-info/PKG-INFO
writing top-level names to biom_format.egg-info/top_level.txt
writing dependency_links to biom_format.egg-info/dependency_links.txt
writing entry points to biom_format.egg-info/entry_points.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'biom_format.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'docs/_build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
writing manifest file 'biom_format.egg-info/SOURCES.txt'
copying biom/_filter.c -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/_filter.pyx -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/_subsample.c -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/_subsample.pyx -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/_transform.c -> build/lib.macosx-10.10-x86_64-2.7/biom
copying biom/_transform.pyx -> build/lib.macosx-10.10-x86_64-2.7/biom
running build_ext
building 'biom._filter' extension
creating build/temp.macosx-10.10-x86_64-2.7
creating build/temp.macosx-10.10-x86_64-2.7/biom
clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch x86_64 -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c biom/_filter.c -o build/temp.macosx-10.10-x86_64-2.7/biom/_filter.o
biom/_filter.c:258:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
^
1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Failed building wheel for biom-format
Running setup.py clean for biom-format
Failed to build biom-format
Installing collected packages: scipy, pyqi, biom-format
Found existing installation: scipy 0.12.0
Uninstalling scipy-0.12.0:
Exception:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 209, in main
status = self.run(options, args)
File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 317, in run
prefix=options.prefix_path,
File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 726, in install
requirement.uninstall(auto_confirm=True)
File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 746, in uninstall
paths_to_remove.remove(auto_confirm)
File "/usr/local/lib/python2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove
renames(path, new_path)
File "/usr/local/lib/python2.7/site-packages/pip/utils/__init__.py", line 267, in renames
shutil.move(old, new)
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 300, in move
rmtree(src)
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/scipy-0.12.0-py2.7.egg-info/dependency_links.txt'
N85566:~ smitra$
============
Another matter,
I tried to update numpy, which seems worked..but still shows me the earlier version. This is what I did.
=========
N85566:~ smitra$ pip install numpy --upgrade
Collecting numpy
Downloading numpy-1.11.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.9MB)
100% |████████████████████████████████| 3.9MB 347kB/s
Installing collected packages: numpy
Found existing installation: numpy 1.7.1
Uninstalling numpy-1.7.1:
Exception:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 209, in main
status = self.run(options, args)
File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 317, in run
prefix=options.prefix_path,
File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 726, in install
requirement.uninstall(auto_confirm=True)
File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 746, in uninstall
paths_to_remove.remove(auto_confirm)
File "/usr/local/lib/python2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove
renames(path, new_path)
File "/usr/local/lib/python2.7/site-packages/pip/utils/__init__.py", line 267, in renames
shutil.move(old, new)
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 300, in move
rmtree(src)
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/numpy-1.7.1-py2.7.egg-info/dependency_links.txt'
N85566:~ smitra$
N85566:~ smitra$ python -c "import numpy; print numpy.version.version"
1.7.1
N85566:~ smitra$
==========
Any problem with PATH might be??
Please help me to fix this issue. Thanks, Mitra
I also had the same problem.
try this command:
sudo pip install -Iv https://pypi.python.org/packages/source/b/biom-format/biom-format-1.3.0.tar.gz#md5=bd35f9b7e1c7daf244fe2dffb2777606
hope to be helpful.
Adrian