Fatal error yaml h no such file or directory

OS X 10.7.3: error: yaml.h: No such file or directory #2

I am having the following issue installing pushserver on OS X 10.7.3.
How serious is this. The pushserver seems to be working.

$ pip install django-pushserver
Downloading/unpacking django-pushserver
Downloading django-pushserver-0.1.2.tar.gz
Running setup.py egg_info for package django-pushserver

Requirement already satisfied (use —upgrade to upgrade): Django>=1.2 in ./lib/python2.7/site-packages (from django-pushserver)
Downloading/unpacking py-hbpush==0.1.0 (from django-pushserver)
Downloading 0.1.0-mitar
Running setup.py egg_info for package py-hbpush

Downloading/unpacking PyYAML (from py-hbpush==0.1.0->django-pushserver)
Downloading PyYAML-3.10.tar.gz (241Kb): 241Kb downloaded
Running setup.py egg_info for package PyYAML

Downloading/unpacking brukva>=0.0.1 (from py-hbpush==0.1.0->django-pushserver)
Downloading bff451511a3cc09cd52bebcf6372a59d36567827
Running setup.py egg_info for package brukva

Downloading/unpacking tornado>0.2 (from py-hbpush==0.1.0->django-pushserver)
Downloading tornado-2.2.tar.gz (330Kb): 330Kb downloaded
Running setup.py egg_info for package tornado

Installing collected packages: django-pushserver, py-hbpush, PyYAML, brukva, tornado
Running setup.py install for django-pushserver

Running setup.py install for py-hbpush
changing mode of build/scripts-2.7/hbpushd from 644 to 755

Running setup.py install for PyYAML
checking if libyaml is compilable
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c build/temp.macosx-10.7-intel-2.7/check_libyaml.c -o build/temp.macosx-10.7-intel-2.7/check_libyaml.o
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:2:18: error: yaml.h: No such file or directory
build/temp.macosx-10.7-intel-2.7/check_libyaml.c: In function ‘main’:
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: ‘yaml_parser_t’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: (Each undeclared identifier is reported only once
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: for each function it appears in.)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: expected ‘;’ before ‘parser’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:6: error: ‘yaml_emitter_t’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:6: error: expected ‘;’ before ‘emitter’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:8: warning: implicit declaration of function ‘yaml_parser_initialize’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:8: error: ‘parser’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:9: warning: implicit declaration of function ‘yaml_parser_delete’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:11: warning: implicit declaration of function ‘yaml_emitter_initialize’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:11: error: ‘emitter’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:12: warning: implicit declaration of function ‘yaml_emitter_delete’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:2:18: error: yaml.h: No such file or directory
build/temp.macosx-10.7-intel-2.7/check_libyaml.c: In function ‘main’:
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: ‘yaml_parser_t’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: (Each undeclared identifier is reported only once
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: for each function it appears in.)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:5: error: expected ‘;’ before ‘parser’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:6: error: ‘yaml_emitter_t’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:6: error: expected ‘;’ before ‘emitter’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:8: warning: implicit declaration of function ‘yaml_parser_initialize’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:8: error: ‘parser’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:9: warning: implicit declaration of function ‘yaml_parser_delete’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:11: warning: implicit declaration of function ‘yaml_emitter_initialize’
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:11: error: ‘emitter’ undeclared (first use in this function)
build/temp.macosx-10.7-intel-2.7/check_libyaml.c:12: warning: implicit declaration of function ‘yaml_emitter_delete’
lipo: can’t open input file: /var/folders/4v/yf_xmfb10d7fcvpn592yqslhlgssbp/T//cc842eYi.out (No such file or directory)

Running setup.py install for brukva

Running setup.py install for tornado

Successfully installed django-pushserver py-hbpush PyYAML brukva tornado
Cleaning up.

Источник

Cannot load CLoader #108

Hi, I’m using pyyaml in a Docker container based on bitnami/minideb:jessie, where python version is 2.7.9.

The original code is using CLoader and I cannot change it. Any reason CLoader fails to load but Loader is fine ?

I cannot figure out what I’m missing here. Any idea ?

Running it from the Docker image python:2.7.9 does not raise any error then:

Thanks for your help.

The text was updated successfully, but these errors were encountered:

Any news on this one? I experience the same error, CLoader does not exist.

I think the whole cyaml is missing. Why is that?

This is because cyaml is optional and requires build dependencies, such as cython and yaml.h to be available upon building the package ( yaml.h comes from libyaml-dev package in Debian/Ubuntu):

This is what it prints when libyaml-dev is not found when running $ pip —no-cache-dir install —verbose —force-reinstall -I pyyaml

And this is what you’ll see if everything is set up fine:

Thanks for the fix! This worked. But I would propose to add such a statement directly in the error message. So if cyaml cannot be compiled but is accessed, it should not just be an attribute not found -error but rather a message telling the above.

Met with the same problem after installing the pyyaml using»pip3 install pyyaml». So I install yaml from source and fix the problem. See https://github.com/yaml/pyyaml.
Download the source code, run
python3 setup.py install —record record.txt
If you met with problems like Permission denied: ‘/usr/local/lib/python3.5/dist-packages/cython.py’
run
python3 setup.py install —record record.txt —user
If you want to uninstall, run
cat record.txt | xargs rm -rf

Ran into the same issue as well. I did bad searching, so did not come across this until after I (re) solved it on my own:
https://gist.github.com/EricCousineau-TRI/15cbc5a7ee7223871e384b5ab3e92e62#gistcomment-3352386

This is the minimum to get CLoader compiled and installed as of July 2020.
https://stackoverflow.com/a/62543781/243431

Closing, as this isn’t really a pyyaml bug, just missing deps to the builds. We might accept docs PRs to update the native extension build deps for various distros, but it’ll be an endless game of whack-a-mole.

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Building fails with Boost 1.67 because of old yaml-cpp #18

I am trying to build the OpenFOAM adapter to run the tutorial https://github.com/precice/precice/wiki/Tutorial-for-CHT-with-OpenFOAM-and-CalculiX. I am doing this from a docker container with ubuntu16.04. I successfully installed:

1. OpenFOAM under /opt/OpenFOAM/
2. CalculiX
3. Precice under /opt/precice-1.1.1

And I successfully made the CalculiX adapter ccx_preCICE.

I installed yaml with apt-get install libyaml-cpp-dev and also building it manually, which worked for the CalculiX adapter.

However, when I run ./Allwmake I get the following error in the wmake.log file:

The standard output when I run ./Allwmake is:

Could you please give me a hint as to what is going wrong?

Thank you very much!

The text was updated successfully, but these errors were encountered:

what version of Boost are you using?

Thank you very much for the quick response. I am using boost_1_67_0 from https://www.boost.org/users/download/ following option 2 in https://github.com/precice/precice/wiki/Dependencies#boost

When I use the debug branch I get this fatal error message:

fatal error: yaml-cpp/yaml.h: No such file or directory

This happens when making CHT.o, however, SinkTemperature.o, HeatFlux.o KappaEffective.o and some other where compiled correctly.

Oh, then probably there is some incompatibility between yaml-cpp and Boost. How did you install yaml-cpp? Boost tends to change frequently, so you may need to build a previous version (for sure Boost 1.65.1 works, that’s what I use).

Could you please upload your Dockerfile (or a minimal working example of it)? It would be much easier for me to help you then! 🙂

Or maybe build the very latest yaml-cpp from source, I guess this requires less work, as you only need to rebeuild the adapter then.

There are also some experimental Dockerfiles in this repository. I am not sure about their state at the moment, but you could get some ideas. However, I am interested in debugging this.

I will test Boost 1.67 now.

1. I installed yaml-cpp from source:

This worked for calculix but I then used.

. This changed the error from.

. to the one on my first post.

I will now try Boost 1.65.1.

I did not make a docker yet but I am using this container avidalto/openfoam5_calculix_precice:v4 where everything is installed under /opt.

These are more or less the commands I used:

/.bashrc of5x cp ccx-212-patch-PW.tgz /opt tar -zxf ccx-212-patch-PW.tgz rm ccx-212-patch-PW.tgz apt-get install -y —no-install-recommends gfortran apt-get install -y —no-install-recommends make apt-get install -y —no-install-recommends f2c apt-get install -y —no-install-recommends liblapack3 apt-get install -y —no-install-recommends liblapack-dev apt-get install -y —no-install-recommends libexodusii-dev apt-get install -y —no-install-recommends libgl1-mesa-dev apt-get install -y —no-install-recommends libglu1-mesa-dev apt-get install -y —no-install-recommends libxi-dev apt-get install -y —no-install-recommends libxmu-dev apt-get install -y —no-install-recommends time apt-get install -y —no-install-recommends python-minimal apt-get install -y —no-install-recommends python apt-get install -y —no-install-recommends python-pip pip install —upgrade pip cd /opt/ccx-212-patch-PW/spooles.2.2/ make lib cd MT/src/ make cd /opt/ccx-212-patch-PW/ARPACK/ make lib # make clean # Maybe later cd /opt/ccx-212-patch-PW/src make mkdir /opt/CalculiX-2.12-executables/ cp /opt/ccx-212-patch-PW/src/ccx_2.12_MT /opt/CalculiX-2.12-executables/ cd /opt # PATH !! export PATH=»/opt/CalculiX-2.12-executables:$» # Install precice dependencies apt update apt install -y build-essential apt install -y scons apt install -y libeigen3-dev apt install -y libxml2-dev apt install -y petsc-dev apt install -y python-dev apt install -y python-numpy cp boost_1_67_0.tar.gz /opt cd /opt tar -xvzf boost_1_67_0.tar.gz cd boost_1_67_0 ./bootstrap.sh —with-libraries=log,thread,system,filesystem,program_options,test —prefix=/usr/local ./b2 install #rm -r boost** ldconfig echo export CPLUS_INCLUDE_PATH=»/usr/include/eigen3:$CPLUS_INCLUDE_PATH» >>

/.bashrc echo export PETSC_DIR=/usr/lib/petscdir/3.6.2/ >>

/.bashrc echo export PETSC_ARCH=x86_64-linux-gnu-real >>

/.bashrc # Install precice. FAILS WITH VERSION 1.0.0 . cd /opt apt-get install -y wget # replace 1.1.1 with actual version wget https://github.com/precice/precice/archive/v1.1.1.tar.gz tar -xzvf v1.1.1.tar.gz cd precice-1.1.1 echo export PRECICE_ROOT=`pwd` >>

/.bashrc # When running SCons to build preCICE, don’t build the tests target. For example, run it like this (specified targets, but only solib and symlink): scons compiler=mpic++ petsc=yes python=no -j 4 solib symlink # Recommended # Run tests #./tools/compileAndTest.py -t # Only for the tests you need python 3 #apt-get install -y python3 #./tools/compileAndTest.py -t # Cant run as root need to add: —allow-run-as-root #./tools/compileAndTest.py -t —allow-run-as-root # Doesn’t work either #sed -i — ‘s// —allow-run-as-root/g’ ./tools/compileAndTest.py # Error: # mpirun was unable to launch the specified application as it could not access # or execute an executable: # Executable: ../build/last/testprecice #rm /opt/v1.1.1.tar.gz # Add $PRECICE_ROOT/build/last to your dynamic library path # As a dynamic library: Add $PRECICE_ROOT/build/last/ to your dynamic library path echo export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PRECICE_ROOT/build/last/ >>

/.bashrc # Try to build yaml manually cd /opt #mkdir yaml git clone https://github.com/jbeder/yaml-cpp.git cd yaml-cpp mkdir build cd build cmake -DBUILD_SHARED_LIBS=ON .. # Need to do make now. Uncomment below make cd .. #rm -r build # Lets try with the calculix adapter cd /opt git clone https://github.com/precice/calculix-adapter.git cd calculix-adapter git checkout -b v2.12 origin/v2.12 sed -i — ‘s|$(HOME)/PathTo/yaml-cpp|/opt/yaml-cpp|g’ Makefile sed -i — ‘s|$(HOME)/PathTo/preCICE|/opt/precice-1.1.1|g’ Makefile sed -i — ‘s|$(HOME)/PathTo/ARPACK|/opt/ccx-212-patch-PW/ARPACK|g’ Makefile sed -i — ‘s|$(HOME)/PathTo/SPOOLES|/opt/ccx-212-patch-PW/spooles.2.2|g’ Makefile sed -i — ‘s|$(HOME)/PathTo/CalculiX/ccx_2.12/src|/opt/ccx-212-patch-PW/src|g’ Makefile make # Fails but . cd /opt/ccx-212-patch-PW/ARPACK cp libarpack_linux.a libarpack_INTEL.a cd /opt/calculix-adapter make # Works # Building openfoam adapter cd /opt mkdir openfoam-adapter cd openfoam-adapter git clone https://github.com/precice/openfoam-adapter.git . apt-get install -y libyaml-cpp-dev ./Allwmake # Error: #/opt/OpenFOAM/OpenFOAM-5.x/wmake/rules/General/transform:25: recipe for target ‘Make/linux64GccDPInt64Opt/CHT/CHT.o’ failed #make: *** [Make/linux64GccDPInt64Opt/CHT/CHT.o] Error 1 source

I also tried similar steps with the dev and FSI branches.

Thank you for the docker files. I will take a look at them to see if a figure out another way of building the openfoam adapter.

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fatal error: yaml.h: No such file or directory about c HOT 1 CLOSED

Actually, issue can be solved by installing libyaml-dev

• Is there an api to get node status? HOT 9
• Unexpected processing behavior of null value in yaml/json HOT 5
• [CPP] Keyword namespace conflicted in cpp
• How to get the content of condition in v1_node_status_t structure, condition is a list_t * HOT 6
• How to get node status (include «Ready» or «Notready») like using «kubectl get nodes” wiht “C api” ？ HOT 6
• CoreV1API_listNamespacedEvent doesn’t work as expected HOT 5
• Regarding Event Internals (Event broadcaster, Event recorder) for C client HOT 5
• Request to generate the C client library based on v1.25.2 HOT 2
• Feature request, add lua support HOT 3
• v0.5.0 release plan HOT 2
• How to update namespaced Custom Resource status with Kubernetes client in C? HOT 3
• Unit test tool for c client HOT 1
• How to set up a non-root user, to use the C API or k8s HOT 5
• EventsV1API_patchNamespacedEvent returns error — cannot unmarshal object into Go value of type jsonpatch.Patch HOT 3
• BUILD.Bazel rule support in c k8s client HOT 8
• Cannot delete pod forcibly with CoreV1API_deleteNamespacedPod API HOT 3
• How can I use Node Proxy Api? HOT 6
• Unexpected processing behavior of null value(string type) in yaml/json HOT 1
• Load of users with client-certificate and client-key paths HOT 6
• pod exec returns truncated output HOT 1

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Yocto system common build errors

1 Hardware resources

Yocto builds may strongly impact your HW resources in terms of

• required disk space
• required RAM
• CPU overheating

1.1 Required disk space

Since Yocto will download the source code that will be used to build the packages included in the image, consider reserving at least 300 GB of free space.

Using a SSD will extremely speed up the build.

1.2 Required RAM

Yocto will check for the host CPU feature and will try to use all of them in order to speed-up the build.

Just as an example,

• with an i7-7700K (4 cores / 8 threads), Yocto will activate 8 building threads
• with an i7-9700K (8 cores / 8 threads), Yocto will activate 8 building threads
• with an i7-11700K (8 cores / 16 threads), Yocto will activate 16 building threads

Each building thread will require a dedicated amount of RAM, that can easily rise above 3 GB.

To safely run 8 building threads, plan to have 32 (8*4) GB of RAM.

To safely run 16 building threads, plan to have 64 (16*4) GB of RAM.

Since such an amount of RAM is not always available, you can forcibly reduce the number of building threads by setting the variable BB_NUMBER_THREADS in your local.conf to something like (available RAM in GB / 4). This also means that is not reasonable run a Yocto build with less then 4 GB of RAM.

A typical settings for a 16 GB RAM system is

BB_NUMBER_THREADS = "4"

Typical errors due to low memory are

collect2: fatal error: ld terminated with signal 9 [Killed]
compilation terminated.

or:

ERROR: Worker process (12928) exited unexpectedly (-9), shutting down...
ERROR: Worker process (12928) exited unexpectedly (-9), shutting down...
...

or:

fatal error: Killed signal terminated program
compilation terminated.

1.3 CPU overheating

Being Yocto extremely resource hungry, a build can easily lead the building host to an overheat condition, with merely unpredictable side effects, ranging from crashes to memory corruptions.

We strongly suggest to keep the CPU core temperature under control.

2 Fetching problems

2.1 GitHub: unsafe repositories

On April 12, 2022, GitHub announced the need to upgrade the local installation of Git. For more information, please see https://github.blog/2022-04-12-git-security-vulnerability-announced/

Something reasonably changed also in GitHub repositories: starting from the above date, some GitHub users are experiencing error messages like

fatal: unsafe repository ('<repo-path>' is owned by someone else)
To add an exception for this directory, call:
    git config --global --add safe.directory <repo-path>  

The message already suggests the solution with the «git config» command, but if this is not working, you may want to updated to latest Git version.

On an Ubuntu machine, you can run

sudo add-apt-repository ppa:git-core/ppa -y
sudo apt update
sudo apt upgrade -y
git config --global --add safe.directory '*'

This will update to the latest git version available for your machine and disable the safe check system-wide.

Please note that the option to disable the safe check system-wide is only available starting from Git v2.35.3

2.2 GitHub: Git protocol on port 9418

On January 11, 2022, Github disabled the Git protocol on 9418. For more information, please see https://github.blog/2021-09-01-improving-git-protocol-security-github/

This change will break all recipes using the Git protocol. Fortunately, starting in Yocto Pyro, Yocto will try fetching using HTTPS when the Git protocol fails. See: https://git.yoctoproject.org/poky/commit/meta/classes/mirrors.bbclass?h=pyro&id=85c41bfcf2c62e8b394a7f3d9efdf50af77ff960

For Yocto Morty and older, you will observe the following error:

fatal: remote error:
The unauthenticated git protocol on port 9418 is no longer supported.
Please see https://github.blog/2021-09-01-improving-git-protocol-security-github/ for more information.

This can be fixed by manually adding HTTPS mirrors to conf/local.conf:

MIRRORS += "
git://anonscm.debian.org/.*   git://anonscm.debian.org/git/PATH;protocol=https n 
git://git.gnome.org/.*        git://git.gnome.org/browse/PATH;protocol=https n 
git://git.savannah.gnu.org/.* git://git.savannah.gnu.org/git/PATH;protocol=https n 
git://git.yoctoproject.org/.* git://git.yoctoproject.org/git/PATH;protocol=https n 
git://.*/.*                   git://HOST/PATH;protocol=https n 
"

2.3 Firewalls / proxies constraints

Firewalls and proxies may block the access to specific websites or protocols (like git).

Double check with the IT team that you are not experiencing any access restriction during the fetching phase.

2.4 Certificates validation

Messages like

server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none

indicate that the certificates on your machine are outdated.

You can try the following commands:

$ sudo apt update
$ sudo apt upgrade

and then check if the latest version of the CAcertificate package can solve the problem.

Note that starting from January 2022, github dropped git:// support and now only https:// (encrypted) access is allowed.

If your Ubuntu release reached its EOL, no further CA certificates updates are available: the installed certificates will systematically expire.

In such case, to avoid git cloning errors, disable https verification (based on CA certificates) by running:

$ git config --global http.sslverify "false"

2.5 Can’t find package

Due to server maintenance sometime it will fail to fetch the source.

Search the exact file name and version and download it from other source into your download directory.

2.6 Checksum mismatch

Sometime you will get an error as listed below.
The reason is due to re packaging on the server of the provider.
locate the pacakage bb file

$ find ../sources/ -name evtest*

./meta-openembedded/meta-oe/recipes-support/evtest
./meta-openembedded/meta-oe/recipes-support/evtest/evtest_1.25.bb

edit the pacakage

$ gedit ./meta-openembedded/meta-oe/recipes-support/evtest/evtest_1.25.bb

And replace:
SRC_URI[archive.md5sum] = «770d6af03affe976bdbe3ad1a922c973»
SRC_URI[archive.sha256sum] = «3d34123c68014dae6f7c19144ef79ea2915fa7a2f89ea35ca375a9cf9e191473»
With:
SRC_URI[archive.md5sum] = «0ef3fe5e20fa2dee8994827d48482902»
SRC_URI[archive.sha256sum] = «6e93ef54f0aa7d263f5486ce4a14cac53cf50036bfd20cf045fef2b27ee6664b»

2.6.1 Error log example

3 kernel compile errors

Some users reported the following error

fatal error: yaml.h: No such file or directory

Although most of the distro already provide the relevant packages, some do not.
Running the following command on the host PC should fix the problem

$ sudo apt install libyaml-dev

4 UBI size is too small (max_leb_cnt too low)

Sometimes when building a large image the system fails, because the image cannot fit into the default 512MB NAND flash.

Log data follows:
| DEBUG: Executing python function set_image_size
| DEBUG: Python function set_image_size finished
| DEBUG: Executing shell function do_image_ubi
| Error: max_leb_cnt too low (4094 needed)
| ERROR: Function failed: do_image_ubi

There are three ways to overcome this issue:

• If you are using a SOM with eMMC, use the eMMC to store the filesystem, and remove the ubi image type from the build process by adding the following line to the conf/local.conf file in your build directory:

IMAGE_FSTYPES_remove_<MACHINE> = "ubi multiubi"

(Replace <MACHINE> with either var-som-mx6, imx6ul-var-dart or var-som-mx7, according to the SOM you are using)

• If you have a SOM with a 512MB NAND flash and no eMMC, you’ll have to remove packages from the image you are building in order to make it fit, or just use a different and smaller image.
• If you have a 1GB NAND flash on the SOM and you want to use it to hold the filesystem, edit the conf/machine/include/variscite.inc file under meta-variscite, comment out the 512MB NAND parameters and uncomment the appropriate 1GB NAND parameters.