I am attempting to build the CORBA omniORB packages on CentOS 7.
I manage to build the RPM, but when I go to install it, it lists failed dependencies that are part of the RPM itself!
I am hoping someone might be able to suggest what to check!
$ sudo rpm -i omniORB-4.2.2-1.x86_64.rpm
error: Failed dependencies:
libCOS4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libCOSDynamic4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomniCodeSets4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomniConnectionMgmt4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomniDynamic4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomniORB4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomniZIOP4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomniZIOPDynamic4.so.2()(64bit) is needed by omniORB-4.2.2-1.x86_64
libomnithread.so.4()(64bit) is needed by omniORB-4.2.2-1.x86_64
$ rpm -qpl omniORB-4.2.2-1.x86_64.rpm | grep -e "lib.*so"
/opt/omniORB-4.2.2/lib/libCOS4.so
/opt/omniORB-4.2.2/lib/libCOS4.so.2
/opt/omniORB-4.2.2/lib/libCOS4.so.2.2
/opt/omniORB-4.2.2/lib/libCOSDynamic4.so
/opt/omniORB-4.2.2/lib/libCOSDynamic4.so.2
/opt/omniORB-4.2.2/lib/libCOSDynamic4.so.2.2
/opt/omniORB-4.2.2/lib/libomniCodeSets4.so
/opt/omniORB-4.2.2/lib/libomniCodeSets4.so.2
/opt/omniORB-4.2.2/lib/libomniCodeSets4.so.2.2
/opt/omniORB-4.2.2/lib/libomniConnectionMgmt4.so
/opt/omniORB-4.2.2/lib/libomniConnectionMgmt4.so.2
/opt/omniORB-4.2.2/lib/libomniConnectionMgmt4.so.2.2
/opt/omniORB-4.2.2/lib/libomniDynamic4.so
/opt/omniORB-4.2.2/lib/libomniDynamic4.so.2
/opt/omniORB-4.2.2/lib/libomniDynamic4.so.2.2
/opt/omniORB-4.2.2/lib/libomniORB4.so
/opt/omniORB-4.2.2/lib/libomniORB4.so.2
/opt/omniORB-4.2.2/lib/libomniORB4.so.2.2
/opt/omniORB-4.2.2/lib/libomniZIOP4.so
/opt/omniORB-4.2.2/lib/libomniZIOP4.so.2
/opt/omniORB-4.2.2/lib/libomniZIOP4.so.2.2
/opt/omniORB-4.2.2/lib/libomniZIOPDynamic4.so
/opt/omniORB-4.2.2/lib/libomniZIOPDynamic4.so.2
/opt/omniORB-4.2.2/lib/libomniZIOPDynamic4.so.2.2
/opt/omniORB-4.2.2/lib/libomnithread.so
/opt/omniORB-4.2.2/lib/libomnithread.so.4
/opt/omniORB-4.2.2/lib/libomnithread.so.4.0
/opt/omniORB-4.2.2/lib64/python2.7/site-packages/_omniidlmodule.so
/opt/omniORB-4.2.2/lib64/python2.7/site-packages/_omniidlmodule.so.4
/opt/omniORB-4.2.2/lib64/python2.7/site-packages/_omniidlmodule.so.4.2
Thanks for any help!
Related
at the moment I'm facing some problems compiling (and running) a (huge) own project with support of Tensorflow. On my own system (Ubuntu 16.04 LTS) everything works fine. Same procedure on a cluster leads to a compile error and I'm not able to find a solution yet.
System information
Have I written custom code: YES
OS Platform and Distribution (e.g., Linux Ubuntu 16.04): CentOS 7.4.1708
TensorFlow installed from (source or binary): source (using the git repo)
TensorFlow version (use command below): 1.9
Python version: 2.7.15
Bazel version (if compiling from source): 0.16
GCC/Compiler version (if compiling from source): 7.30
CUDA/cuDNN version: not used
GPU model and memory: Tesla K20m
Exact command to reproduce:
Cloned tensorflow repo from github
Configure Bazel (./configure in tensorflow repo)
Built libtensorflow_cc.so with bazel (worked fine!!!)
Downloaded dependencies with delivered script tensorflow/contrib/makefile/download_dependencies.sh
(tried installing protobuf & eigen manually, too)!
Installed protobuf with ./autogen.sh && ./configure && make && make install
Installed Eigen from downloaded dependencies
Copied libraries, headers and includes into own project:
$ cp bazel-bin/tensorflow/libtensorflow_cc.so ../tf_project/lib/
$ cp bazel-bin/tensorflow/libtensorflow_framework.so ../tf_project/lib/
$ cp /tmp/proto/lib/libprotobuf.a ../tf_project/lib/
$ mkdir -p ../tf_project/include/tensorflow
$ cp -r bazel-genfiles/ * ../tf_project/include/
$ cp -r tensorflow/cc ../tf_project/include/tensorflow
$ cp -r tensorflow/core ../tf_project/include/tensorflow
$ cp -r third_party ../tf_project/include
$ cp -r /tmp/proto/include/ * ../tf_project/include
$ cp -r /tmp/eigen/include/eigen3/ * ../tf_project/include
Remark: On my own system it works this way for weeks now. I can use tensorflow in my own project with an exported model trained with keras inside a python project. I make predictions using client_sessions and many other functions of the tensorflow framework and it works properly.
Problem: At the cluster I can compile tensorflow as dynamic library, install protobuf and eigen.
When I try to compile my project (similar process regarding my own system) without significant changes it doesn't work and stops with following error message:
.../tensorflow/include/tensorflow/core/framework/tensor.pb.h:12:2: error: #error This file was generated by a newer version of protoc which is
#error This file was generated by a newer version of protoc which is
^~~~~
.../include/tensorflow/core/framework/tensor.pb.h:13:2: error: #error incompatible with your Protocol Buffer headers. Please update
#error incompatible with your Protocol Buffer headers. Please update
^~~~~
.../include/tensorflow/core/framework/tensor.pb.h:14:2: error: #error your headers.
#error your headers.
^~~~~
.../include/tensorflow/core/framework/tensor.pb.h:27:10: fatal error: google/protobuf/inlined_string_field.h: No such file or directory
#include <google/protobuf/inlined_string_field.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
So, clearly this should be the issue:
This file was generated by a newer version of protoc which is incompatible with your Protocol Buffer headers. Please update your headers.
and
fatal error: google/protobuf/inlined_string_field.h: No such file or directory
Tried solutions:
I tried different versions of protobuf but there was an error every single try.
I tried installing protobuf and eigen manually (without the download_dependencies.sh script)
I'm wondering because my own installation following exact the same steps works properly. Maybe there is an issue with one of the components unless I tried different versions to make sure that these aren't "new" issues.
Can someone help me solving this error that I can compile and run this project at the other machine?
Looking forward to get helpful solutions :) Thank you very much for the support!
Best regards from Germany!
First, I checked on github, tensorflow r1.9 requires protobuf >=3.6.0. With download_dependencies.sh script, you always get protobuf 3.5.0, in which lack of inlined_string_field.h and some other headers.
Second, some errors that ask you to update protobuf version. I tried many versions of protobuf too. Only version 3.6.0 works well, rather than version 3.6.1 or older ones.
For these errors,
error This file was generated by a newer version of protoc which is
fatal error: google/protobuf/inlined_string_field.h: No such file or directory
It is a mismatch version problem. My solutions is that manually download protobuf 3.6.0 from
https://github.com/protocolbuffers/protobuf/releases/download/v3.6.0/protoc-3.6.0-linux-x86_64.zip
install it and cp /usr/local/include/google to somewhere/tf/include. It works quite well for me. I don't know if you tried version 3.6.0.
download_dependencies.sh script would provide a mismatch version of
protobuf. See the issue I posted on github
https://github.com/tensorflow/tensorflow/issues/22536
Also, I noticed your copied files are different from mine. I did in this way.
sudo mkdir /usr/local/tensorflow/include
sudo cp -r tensorflow/contrib/makefile/downloads/eigen/Eigen /usr/local/tensorflow/include/
sudo cp -r tensorflow/contrib/makefile/downloads/eigen/unsupported /usr/local/tensorflow/include/
sudo cp -r tensorflow/contrib/makefile/gen/protobuf/include/google /usr/local/tensorflow/include/
sudo cp tensorflow/contrib/makefile/downloads/nsync/public/* /usr/local/tensorflow/include/
sudo cp -r bazel-genfiles/tensorflow /usr/local/tensorflow/include/
sudo cp -r tensorflow/cc /usr/local/tensorflow/include/tensorflow
sudo cp -r tensorflow/core /usr/local/tensorflow/include/tensorflow
sudo mkdir /usr/local/tensorflow/include/third_party
sudo cp -r third_party/eigen3 /usr/local/tensorflow/include/third_party/
sudo mkdir /usr/local/tensorflow/lib
sudo cp bazel-bin/tensorflow/libtensorflow_*.so /usr/local/tensorflow/lib
Btw, I run build_all_linux.sh instead of download_dependencies.sh.
I hope it will be helpful for you.
I meet this problem before, following is my solution:
I successfully built tensorflow-r1.8 with bazel. And I found protoc in following path is 3.5.0:
/home/zsb/.cache/bazel/_bazel_zsb/1372f28eb0671f692e7ac38330377d8c/execroot/org_tensorflow/bazel-out/host/bin/external/protobuf_archive/protoc --version
but actually my system config is using protoc version 3.4.0
I confirmed this by type "protoc --version" directly.
So finally I update system protobuffer version to 3.5.0 and this problem fixed.
I want to be able to make and run this particular library on my computer. Currently going through the INSTALL file. I am currently at the point:
After extracting the Poco (Complete Edition) source archive, the configure
script should be called with the following parameters:
./configure --omit=Crypto,Net,NetSSL_OpenSSL,Data/ODBC,Data/MySQL \
--no-tests --no-samples
This line avoids building the parts of Poco which are dependent on third-party
libraries, and are not required for openBliSSART.
You can also specify a prefix where Poco should be installed, but in most cases
you should leave the default /usr/local.
I can't seem to run the options, so I simply ran ./configure, this seemed to have worked till the point where I encountered:
checking for fftw_plan_dft_r2c_1d in -lfftw3... yes
checking for Poco (Enterprise)... no
configure: error: Need Poco Enterprise v1.3.6+!
But the fact is, that I have installed Poco already on the system through a brew install poco and downloaded the library from their source website and compiled it ground up. looking back at INSTALL:
Depending on where you have installed Poco, you may have to set the
LD_LIBRARY_PATH environment variable to contain the Poco "lib" directory,
or run the ldconfig tool. The following lines work with Ubuntu and openSUSE
($ indicates the shell prompt):
$ sudo sh -c 'echo <prefix>/lib > /etc/ld.so.conf.d/poco.conf'
$ sudo ldconfig
where <prefix> is the Poco install prefix (by default /usr/local).
Now when I do a simple sudo find / -name poco, I get:
/usr/local/var/homebrew/linked/poco
/usr/local/opt/poco
/usr/local/Cellar/poco
find: /private/var/db/ConfigurationProfiles/Store: Operation not permitted
find: /private/var/folders/pq/xchc5hxj02d754txf8nml5f00000gn/0/SafariFamily: Operation not permitted
find: /private/var/folders/pq/xchc5hxj02d754txf8nml5f00000gn/0/com.apple.LaunchServices.dv: Operation not permitted
find: /private/var/folders/pq/xchc5hxj02d754txf8nml5f00000gn/0/com.apple.nsurlsessiond: Operation not permitted
find: /private/var/folders/pq/xchc5hxj02d754txf8nml5f00000gn/0/com.apple.routined: Operation not permitted
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000y800007k/0/com.apple.nsurlsessiond: Operation not permitted
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000s4000069/0/com.apple.nsurlsessiond: Operation not permitted
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000s4000069/0/com.apple.routined: Operation not permitted
/Users/sharanduggirala/Library/Logs/Homebrew/poco
/Users/sharanduggirala/Documents/of_v0.9.8_osx_release/libs/poco
/Users/sharanduggirala/Documents/of_v0.9.8_osx_release/scripts/apothecary/formulas/poco
find: /dev/fd/3: Not a directory
find: /dev/fd/4: Not a directory
Also, it looks like while building poco, I did a ./configure --static. Would this have affected my compilation? How do I link this library?
I have already used the command ./configure --with-poco-prefix=/usr/local/opt/poco which doesn't really change anything.
Notes relating to S.M.'s Answer
I tried this, but got the error:
brew install poco --with-static ⏎
==> Downloading https://pocoproject.org/releases/poco-1.9.0/poco-1.9.0-all.tar.gz
######################################################################## 100.0%
Error: SHA256 mismatch
Expected: 028de410fc78d5f9b1ff400e93ec3d59b9e55a0cbbf0d8fec04636882b72ea45
Actual: 0387bf0f9d313e2311742e1ad0b64e07f2f3e76039eed20e3b9aa9951b88e187
Archive: /Users/sharanduggirala/Library/Caches/Homebrew/poco-1.9.0.tar.gz
To retry an incomplete download, remove the file above.
I also tried:
./configure --static ⏎
configure: error: unrecognized option: `--static'
Try `./configure --help' for more information
Do not install poco from sources. Use brew install poco. If you want the same like ./configure --static use brew install poco --with-static.
I have built rpm (Version 4.14.1) with the usual trilogy:
./configure --prefix=/usr
make
make install
This went without error and the rpm executable was installed, as expected, into /usr/bin/rpm.
When I then tried to execute rpm, it wouldn't do anything and exit with Unable to open /usr/local/lib/rpm/rpmrc for reading: No such file or directory..
When I then created a symbolic link ln -s /usr/lib/rpm/rpmrc /usr/local/lib/rpm/rpmrc, the executable rpm could be started.
Is this behaviour expected? Should make install not place the rpmrc file into a place where rpm finds it?
Preface: I am new to OCaml, OPAM, and OASIS.
tldr question: How do I properly set up a package with opam that is not already available in the repository (I can't just do opam install X)? More details follow:
I am trying to include ocaml-glpk in an OCaml project. I installed ocaml-glpk just by running make and make install as stated in the README, and the given example compiles and runs correctly. However, I am using OASIS to generate the build system of my project, and I am not sure how to set it up. I have the same example (renamed to glpkExample.ml in a src folder) and the following in my _oasis file:
Executable "glpkExample"
Path: src
MainIs: glpkExample.ml
CompiledObject: best
BuildDepends:
glpk
After running oasis setup -setup-update dynamic, I run make and get the following error:
ocaml setup.ml -build
Finished, 0 targets (0 cached) in 00:00:00.
+ /home/dimitrios/.opam/system/bin/ocamlfind ocamlopt -g -linkpkg -package glpk src/glpkExample.cmx -o src/glpkExample.native
File "_none_", line 1:
Error: Cannot find file /home/dimitrios/.opam/system/lib/glpk/glpk.cmxa
Command exited with code 2.
Compilation unsuccessful after building 4 targets (3 cached) in 00:00:00.
E: Failure("Command ''/usr/bin/ocamlbuild' src/glpkExample.native -tag debug' terminated with error code 10")
make: *** [build] Error 1
It seems the glpk library is missing a cmxa file needed to compile a native executable. I am not sure how to fix this. To compile glpkExample.ml correctly, my Makefile includes /home/dimitrios/.opam/system/lib/glpk and also uses the OCamlMakefile, which is extremely long and convoluted. Any help on setting this up with OASIS or how to get ocaml-glpk to work nicely with OASIS would be greatly appreciated.
Thanks!
This website is not appropriate for bug reports. You should really report it here.
The temporary solution is to use CompiledObject: byte to compile in bytecode.
If you're using opam then it is best to install application with it, not manually. Try to clean up your system and remove whatever you installed, and then do:
$ eval `opam config env`
$ opam install ocaml-glpk
Afterwards, if glpk is packaged in opam correctly, it should work with your setup, i.e., just with oasis's BuildDepends field and nothing more.
You can consider this a follow-up question to How do I install the OpenSSL C++ library on Ubuntu?
I'm trying to build some code on Ubuntu 10.04 LTS that requires OpenSSL 1.0.0.
Ubuntu 10.04 LTS comes with OpenSSL 0.9.8k:
$ openssl version
OpenSSL 0.9.8k 25 Mar 2009
So after running sudo apt-get install libssl-dev and building, running ldd confirms I've linked in 0.9.8:
$ ldd foo
...
libssl.so.0.9.8 => /lib/i686/cmov/libssl.so.0.9.8 (0x00110000)
...
libcrypto.so.0.9.8 => /lib/i686/cmov/libcrypto.so.0.9.8 (0x002b0000)
...
How do I install OpenSSL 1.0.0 and the 1.0.0 development package?
Update: I'm writing this update after reading SB's answer (but before trying it), because it's clear I need to explain that the obvious solution of downloading and installing OpenSSL 1.0.0 doesn't work:
After successfully doing the following (recommended in the INSTALL file):
$ ./config
$ make
$ make test
$ make install
...I still get:
OpenSSL 0.9.8k 25 Mar 2009
...and:
$ sudo apt-get install libssl-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libssl-dev is already the newest version.
The following packages were automatically installed and are no longer required:
linux-headers-2.6.32-21 linux-headers-2.6.32-21-generic
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
...and (just to make sure) after rebuilding my code, ldd still returns the same thing.
Update #2: I added the "-I/usr/local/ssl/include" and "-L/usr/local/ssl/lib" options (suggested by SB) to my makefile, but I'm now getting a bunch of undefine reference compile errors, for example:
/home/dspitzer/foo/foo.cpp:86: undefined reference to `BIO_f_base64'
/home/dspitzer/foo/foo.cpp:86: undefined reference to `BIO_new'
/usr/local/ssl/include/ contains only an openssl directory (which contains numerous .h files), so I also tried "-I/usr/local/ssl/include/openssl" but got the same errors.
Update #3: I tried changing the OpenSSL includes from (for example):
#include <openssl/bio.h>
...to:
#include "openssl/bio.h"
...in the .cpp source file but still get the same undefined reference errors.
Update #4: I now realize those undefined reference errors are linker errors. If I remove the "-L/usr/local/ssl/lib" from my Makefile, I don't get the errors (but it links to OpenSSL 0.9.8). The contents of /usr/local/ssl/lib/ are:
$ ls /usr/local/ssl/lib/
engines libcrypto.a libssl.a pkgconfig
I added -lcrypto, and the errors went away.
Get the 1.0.0a source from here.
# tar -xf openssl-1.0.0a.tar.gz
# cd openssl-1.0.0a
# ./config
# sudo make install
Note: if you have man pages build errors on modern systems, use make install_sw instead of make install.
This puts it in /usr/local/ssl by default
When you build, you need to tell gcc to look for the headers in /usr/local/ssl/include and link with libs in /usr/local/ssl/lib. You can specify this by doing something like:
gcc test.c -o test -I/usr/local/ssl/include -L/usr/local/ssl/lib -lssl -lcrypto
EDIT DO NOT overwrite any system libraries. It's best to keep new libs in /usr/local. Overwriting Ubuntu defaults can be hazardous to your health and break your system.
Additionally, I was wrong about the paths as I just tried this in Ubuntu 10.04 VM. Fixed.
Note, there is no need to change LD_LIBRARY_PATH since the openssl libs you link against by default are static libs (at least by default - there might be a way to configure them as dynamic libs in the ./config step)
You may need to link against libcrypto because you are using some calls that are built and defined in the libcrypto package. Openssl 1.0.0 actually builds two libraries, libcrypto and libssl.
EDIT 2 Added -lcrypto to gcc line.
Instead of:
$ ./config
$ make
$ make test
$ make install
Do:
$ sudo ./config --prefix=/usr
$ sudo make
$ sudo make test
$ sudo make install
This will help you update to openssl 1.0.1g to patch for CVE-2014-0160 (Heartbleed).
OpenSSL Security Advisory [07 Apr 2014]
TLS heartbeat read overrun (CVE-2014-0160)
A missing bounds check in the handling of the TLS heartbeat extension can be
used to reveal up to 64k of memory to a connected client or server.
Only 1.0.1 and 1.0.2-beta releases of OpenSSL are affected including
1.0.1f and 1.0.2-beta1.
Thanks for Neel Mehta of Google Security for discovering this bug and to
Adam Langley and Bodo Moeller for
preparing the fix.
Affected users should upgrade to OpenSSL 1.0.1g. Users unable to immediately
upgrade can alternatively recompile OpenSSL with -DOPENSSL_NO_HEARTBEATS.
1.0.2 will be fixed in 1.0.2-beta2.
Source: https://www.openssl.org/news/secadv_20140407.txt
Here's what solved it for me:
Upgrade latest version OpenSSL on Ubuntu
Transcribing the main information:
Download the OpenSSL v1.0.0g source:
$ wget http://www.openssl.org/source/openssl-1.0.0g.tar.gz
Unpack the archive and install:
$ tar xzvf openssl-1.0.0g.tar.gz
$ cd openssl-1.0.0g
$ ./config
$ make
$ make test
$ sudo make install
All files, including binaries and man pages are install under the directory /usr/local/ssl. To ensure users use this version of OpenSSL instead of the previous version you must update the paths for man pages and binaries.
Edit the file /etc/manpath.config adding the following line before the first MANPATH_MAP:
MANPATH_MAP /usr/local/ssl/bin /usr/local/ssl/man
Update the man database (I honestly can't remember and don't know for sure if this command was necessary - maybe try without it and at the end when testing if the man pages are still the old versions come back and run mandb):
sudo mandb
Edit the file /etc/environment and insert the path for OpenSSL binaries (/usr/local/ssl/bin) before the path for Ubuntu's version of OpenSSL (/usr/bin). My environment file looks like this:
PATH="/usr/local/sbin:/usr/local/bin:/usr/local/ssl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games"
Logout and login and test:
$ openssl version
OpenSSL 1.0.0g 18 Jan 2012
Also test the man pages by running man openssl and at the very bottom in the left hand corner it should report 1.0.0g.
Note that although the users will now automatically use the new version of OpenSSL, existing programs (e.g. Apache) may not as they are linked against the libraries from the Ubuntu version.