Conda build R package fails at C compiler issue on MacOS Mojave - r

I'm trying to install an R package called treatSens with conda to use it in Jupyter notebook. The commands I executed:
conda install conda-build
conda skeleton cran treatSens
conda build r-treatsens
conda install -c local r-treatsens
And I got the error about C compiler
* installing *source* package ‘dbarts’ ...
** package ‘dbarts’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/Users/myusername/anaconda3/conda-bld/r-dbarts_1543961434509/myenvname':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘dbarts’
My clang version:
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Users/myusername/anaconda3/envs/myenvname/bin
Looking into the config.log file I see
configure:3570: x86_64-apple-darwin13.4.0-clang -V >&5
clang-4.0: error: argument to '-V' is missing (expected 1 value)
clang-4.0: error: no input files
configure:3581: $? = 1
configure:3570: x86_64-apple-darwin13.4.0-clang -qversion >&5
clang-4.0: error: unknown argument: '-qversion'
clang-4.0: error: no input files
configure:3581: $? = 1
configure:3601: checking whether the C compiler works
configure:3623: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -fdebug-prefix-map=/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/work=/usr/local/src/conda/r-dbarts-0.9_5 -fdebug-prefix-map=/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib conftest.c >&5
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
ld: dynamic main executables must link with libSystem.dylib for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
It seems it's a problem about Conda build using the certain version of Apple C compiler. My guess is that I need to customize the C compiler for conda build. So my question becomes
What correct gcc version do I need.
How to set it for conda build.

As a quick and dirty workaround (from this comment), I was able to install packages in R using below code in RStudio (opened in conda env)
Sys.setenv(CONDA_BUILD_SYSROOT="/")
Now, you can install any R package via RStudio Console e.g.
install.packages("tidyverse")
Hope this helps.

There are several things you must do to get things building properly in MacOS Mojave. For reasons mysterious to me, the Anaconda folks are not keen to make this smooth, which is especially maddening for those of us who use esoteric R packages. I will write what seems current as of 2019-04-20:
1. Install Xcode (v10.2.1)
2. Install headers in the place open source tends to expect finding them. From the command line:
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
3. Install the command-line tools
As a belt-and braces approach, I downloaded and installed the DMG Command_Line_Tools_macOS_10.14_for_Xcode_10.2.1 from https://developer.apple.com/download/more/
I believe this is also what is done by xcode-select --install. If you run that command (once the tools are installed), you should see the message
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
4. Download a copy of older MacOS SDK files. For example, from here
5. Create a directory /opt
sudo mkdir /opt
6. Copy the SDK files there
sudo cp -r ~/Downloads/MacOSX10.9.sdk /opt/
sudo chmod -R a+rX /opt
7. Create a conda_build_config.yaml file that will be referenced by Conda-build and related software. It should contain the following
macos_min_version:
- 10.9
macos_machine:
- x86_64-apple-darwin13.4.0
MACOSX_DEPLOYMENT_TARGET:
- 10.9
CONDA_BUILD_SYSROOT: # [osx]
- /opt/MacOSX10.9.sdk # [osx]
In a terminal you can do that with:
mkdir ~/.conda || echo 'Dir already present'
echo "macos_min_version:" >> ~/.conda/conda_build_config.yaml
echo " - 10.9" >> ~/.conda/conda_build_config.yaml
echo "macos_machine:" >> ~/.conda/conda_build_config.yaml
echo " - x86_64-apple-darwin13.4.0" >> ~/.conda/conda_build_config.yaml
echo "MACOSX_DEPLOYMENT_TARGET:" >> ~/.conda/conda_build_config.yaml
echo " - 10.9" >> ~/.conda/conda_build_config.yaml
echo "CONDA_BUILD_SYSROOT:" >> ~/.conda/conda_build_config.yaml
echo " - /opt/MacOSX10.9.sdk" >> ~/.conda/conda_build_config.yaml
8. Tell Conda about your YAML file via your .condarc. It should contain the lines:
conda_build:
config_file: ~/.conda/conda_build_config.yaml
which can be accomplished using
echo "conda_build:" >> ~/.condarc
echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc

Related

Failed to 'pip3 install rpy2' in linux

everyone. I tried to install rpy2 in Centos6.10, with Python 3.6.4 and R version 3.5.2. I used the comand 'pip3 install rpy2'. I got the following errors:
cwd: /tmp/pip-install-7bxzxlni/rpy2_0e939a480cc0488d918a202af1b64127/
Complete output (153 lines):
['cffi>=1.10.0', 'jinja2', 'pytz', 'tzlocal']
running install
running build
cffi mode: CFFI_MODE.ANY
running build_py
file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/rpy2
...(many copy information like this "copying ./rpy2/rinterface_lib/memorymanagement.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface_lib")
file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
generating cffi module 'build/lib.linux-x86_64-3.6/_rinterface_cffi_abi.py'
running build_ext
generating cffi module 'build/temp.linux-x86_64-3.6/_rinterface_cffi_api.c'
creating build/temp.linux-x86_64-3.6
building '_rinterface_cffi_api' extension
creating build/temp.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/temp.linux-x86_64-3.6
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O2 -pipe -fPIC -DRPY2_RLEN_LONG=True -DR_INTERFACE_PTRS=True -Irpy2/rinterface_lib/ -I/home/work/.jumbo/include/python3.6m -c build/temp.linux-x86_64-3.6/_rinterface_cffi_api.c -o build/temp.linux-x86_64-3.6/build/temp.linux-x86_64-3.6/_rinterface_cffi_api.o
In file included from build/temp.linux-x86_64-3.6/_rinterface_cffi_api.c:569:
rpy2/rinterface_lib/R_API.h:199: warning: function declaration isn’t a prototype
In file included from build/temp.linux-x86_64-3.6/_rinterface_cffi_api.c:570:
rpy2/rinterface_lib/R_API_eventloop.h:26: error: redefinition of typedef ‘InputHandler’
rpy2/rinterface_lib/R_API_eventloop.h:8: note: previous declaration of ‘InputHandler’ was here
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/work/.jumbo/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7bxzxlni/rpy2_0e939a480cc0488d918a202af1b64127/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7bxzxlni/rpy2_0e939a480cc0488d918a202af1b64127/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-lx5dv6cc/install-record.txt --single-version-externally-managed --compile --install-headers /home/work/.jumbo/include/python3.6m/rpy2 Check the logs for full command output.
'''
Since there is "command 'gcc' failed with exit status 1", I installed all things mentioned in here. Since "Command errored out with exit status 1", I referred here~, e.g, I have tried 'pip3 install --upgrade rpy2' and I also tried to first upgrade my pip3. But these ways did not help me. Besides, I followed by this way and this~. The first did not help and the latter will pose 'error: option --r-home not recognized' after my command 'python3 setup.py build --r-home /usr/lib64/R/ install'.
Here is some other information:
echo$PATH
bash:echo/home/work/.jumbo/bin/core_perl:/home/work/.jumbo/bin:/home/work/.jumbo/bin/core_perl:/home/work/.jumbo/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/opt/bin:/home/opt/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bin:/home/opt/bin:/usr/local/git/bin:/home/work/bin: No such file or directory
echo$R_HOME
bash: echo/usr/lib64/R: No such file or directory
echo$LD_LIBRARY_PATH
Please help me!
I get my "R_HOME" by starting R and input 'Sys.getenv("R_HOME")'. The output is "/usr/lib64/R". This is why I creat the variable "R_HOME" by "export R_HOME=/usr/lib64/R" in my /etc/profile. Now I use 'which R' and I get '/usr/bin/R', so I changed "R_HOME" variable from "/usr/lib64/R" into "/usr/bin/" which solved my problem! Oh yeah! I hope my experience can help some guys.

"How to fix 'error: command 'gcc' failed with exit status 1' while installing "SudachiPy" python package?

I am working in building Japanese NLP sentiment analysis, to tokenise the Japanese sentence we have a package called "SudachiPy".I tried to install it but I am getting error while installing the package. I'm using anaconda in MAC Book pro.
I tried all the steps mentioned in stack overflow by installing following libraries to debug the error.
pip3 install python3-dev
Also I tried launching an "Ubuntu" instance from AWS and try to install "SudachiPy" but still encountering the same error.
pip3 install SudachiPy
Building wheels for collected packages: dartsclone
Building wheel for dartsclone (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/lf/4754h1x94x39xfw_q6c8_ryc0000gn/T/pip-install-st3sqcmm/dartsclone/setup.py'"'"'; __file__='"'"'/private/var/folders/lf/4754h1x94x39xfw_q6c8_ryc0000gn/T/pip-install-st3sqcmm/dartsclone/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/lf/4754h1x94x39xfw_q6c8_ryc0000gn/T/pip-wheel-x8k1ryul --python-tag cp36
cwd: /private/var/folders/lf/4754h1x94x39xfw_q6c8_ryc0000gn/T/pip-install-st3sqcmm/dartsclone/
Complete output (25 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.6
creating build/lib.macosx-10.7-x86_64-3.6/dartsclone
copying dartsclone/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/dartsclone
running build_ext
cythoning dartsclone/_dartsclone.pyx to dartsclone/_dartsclone.cpp
/anaconda3/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/lf/4754h1x94x39xfw_q6c8_ryc0000gn/T/pip-install-st3sqcmm/dartsclone/dartsclone/_dartsclone.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: dartsclone/_dartsclone.pyx:119:49: local variable 'result' referenced before assignment
warning: dartsclone/_dartsclone.pyx:120:15: local variable 'result' referenced before assignment
building 'dartsclone._dartsclone' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/dartsclone
creating build/temp.macosx-10.7-x86_64-3.6/csrc
creating build/temp.macosx-10.7-x86_64-3.6/csrc/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I./csrc/include -I/anaconda3/include/python3.6m -c dartsclone/_dartsclone.cpp -o build/temp.macosx-10.7-x86_64-3.6/dartsclone/_dartsclone.o
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
dartsclone/_dartsclone.cpp:610:10: fatal error: 'ios' file not found
#include "ios"
^~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for dartsclone
You need to install some deps before, similar to Linux build-essential:
xcode-select install
Also, you may need to specify the right compiler, by setting this env. variable:
CFLAGS='-stdlib=libc++'

Installation of rJava

I've tried to solve this using the previous questions/answers on SO but without any success. So, here's my problem.
I'm using RStudio on and Ubuntu box (14.04) and I tried to upgrade rJava from sources and in the process I managed to lose it.
I tried to install it again using,
install.packages("rJava")
which returned the following error message,
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/darren/R/x86_64-pc-linux-gnu-library/3.2/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
So, I went to the terminal and typed,
sudo R CMD javareconf
which also gave the following error,
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
#include <jni.h>
^
compilation terminated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /usr/lib/jvm/default-java
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
I tried to follow these links, one and two but they didn't seem to resolve my issue; there are more links on SO but I'm not sure which one to follow. I've also un-installed and re-installed RStudio via the Ubuntu Software Centre but this didn't make any difference.
Can anyone else help?
In short, I want to be able to use RStudio with rJava again without it destroying any other uses of Java (such as jmol).
You don't seem to have JDK installed. You will need at least
sudo apt-get install openjdk-7-jdk
then re-run
sudo R CMD javareconf
Make sure you do NOT set JAVA_HOME by hand - it will be detected automatically. You should then see something like this:
$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.7.0_91
Java home path : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/../include
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
What is wrong with sudo apt-get install r-cran-rjava ?
See for example this earlier answer and the question / thread around it.
For an installation from scratch, you could still much worse than starting from sudo apt-get build-dep r-cran-rjava. It will get you the JDK corresponding to your Ubuntu version.
First i would recommend installing Rstudio from its website: https://www.rstudio.com/products/rstudio/download/ (i.e. Rstudio 64bit: https://download1.rstudio.org/rstudio-0.99.489-amd64.deb). This does not solve the problem directly, but it helps to avoid other bugs with Rstudio.
Regarding the error, trying to make sure you have JDK install. I don't think the command java -version can tell if JDK is installed. You have to check the package of JDK itself, or based on the error message, do this:
locate jni.h
The output should match or compatible with your JAVAHOME, e.g:
/usr/lib/jvm/java-7-openjdk-amd64/include/jni.h
/usr/lib/jvm/java-7-oracle/include/jni.h
Update 1:
R CMD javareconf is looking for the jni.h file under $(JAVA_HOME)/include
You have JDK installed, but it is very likely that you are having default java to a JRE directory, that why the error happened.
You can see where default-java is really pointing to by doing this command:
jRealDir=$(readlink -f /usr/lib/jvm/default-java)
echo $jRealDir
# sample correct output: /usr/lib/jvm/jdk1.8.0_65
# or /usr/lib/jvm/java-8-oracle if you default to Oracle's
# now check jni.h
ls -l $jRealDir/include/jni.h
# sample expected output:
# /usr/lib/jvm/jdk1.8.0_65/include/jni.h
If the ls command failed, you have to setup so that javareconf ( and later rJava) can use the java from JDK not from JRE. You have two options:
Method 1: Do it system-wide
This is convenient, but may effect other program like the one you mentioned jmol. But don't worry, this is revertible, just re-run the command and pick the old one. Do the following command and pick the dir that has JDK:
sudo update-alternatives --config java
After that test how jmol works, if it works alright then congrat. You are now ready to test rJava. If not, try the second method below
Method 2: Do it for R only
put this in the .Rprofile under your home directory
Sys.setenv(JAVA_HOME = '/usr/lib/jvm/jdk1.8.0_65')
# this set JAVA_HOME for R to correct java home dir.
After updating or creating the .Rprofile DO restart R in Rstudio. The R CMD javareconf may still fail in this case, but it should be OK if you run it from Shell under Tools menu of Rstudio.
Regarding the installing or Rstudio from Ubuntu's stock repo. It would not make a difference for getting rJava running. Then again, I recommend installing Rstudio for its homepage because new version also has some nice features (i.e. better autocompletion, which I like the most).
Here is link on R-Bloggers that worked for me: https://www.r-bloggers.com/installing-rjava-on-ubuntu/
sudo apt-get install -y default-jre
sudo apt-get install -y default-jdk
sudo R CMD javareconf
install.packages("rJava")
I've been dealing with this exact issue, nothing in this thread or other that are similar have solved it. I'm on Ubuntu 16.04, here's how I got it to work:
apt-get install openjdk-9-jdk
rm -rf /usr/lib/jvm/default-java
ln -s /usr/lib/jvm/java-9-openjdk-amd64/ /usr/lib/jvm/default-java
You can see where the JAVA_HOME is in the error message.
Then use locate jni.h to find where is jni.h, next use soft link to link this location to $(JAVA_HOME)/include, just like #biocyberman mentioned.
This is what I did:
ln -s /usr/lib/jvm/java-8-openjdk-amd64/include/jni.h /opt/conda/include/jni.h
ln -s /usr/lib/jvm/java-8-openjdk-amd64/include/linux/jni_md.h /opt/conda/include/jni_md.h
ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib/
Since my JAVA_HOME is /opt/conda and I also don't have jni_md.h and -ljvm.
I am use Ubuntu 16.04.

Installing package failed when trying to run to application to Meego

I'm trying to run a Hamattan Application on a Meego Device, but everytime I try to run it into the Meego device:
:-1: error: Installing package failed.
always appears. But sometimes when I check my phone the application is there and it's running.
In Settings->Applications->Manage Applications it says there:
Test2
Installation Failed
Please Help me. Thank you very much!
Compile Output:
Running build steps for project test2...
Configuration unchanged, skipping qmake step.
Starting: "C:\qtsdk\madde\bin\make.exe" -w
make: Entering directory `/c/Users/bcue/Qt/test2'
make: Nothing to be done for `first'.
make: Leaving directory `/c/Users/bcue/Qt/test2'
The process "C:\qtsdk\madde\bin\make.exe" exited normally.
Creating package file ...
Package Creation: Running command 'c:/qtsdk/madde/bin/mad dpkg-buildpackage -nc -uc -us'.
dpkg-buildpackage: set CFLAGS to default value: -g -O2
dpkg-buildpackage: set CPPFLAGS to default value:
dpkg-buildpackage: set LDFLAGS to default value:
dpkg-buildpackage: set FFLAGS to default value: -g -O2
dpkg-buildpackage: set CXXFLAGS to default value: -g -O2
dpkg-buildpackage: source package test2
dpkg-buildpackage: source version 0.0.1
dpkg-buildpackage: source changed by unknown <>
dpkg-buildpackage: host architecture armel
which: pgp: unknown command
debian/rules build
make: Nothing to be done for `build'.
debian/rules binary
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
# Add here commands to install the package into debian/test2.
/usr/bin/make INSTALL_ROOT="/c/Users/bcue/Qt/test2"/debian/test2 install
make[1]: Entering directory `/c/Users/bcue/Qt/test2'
install -m 644 -p c:/Users/bcue/Qt/test2/test2.desktop /c/Users/bcue/Qt/test2/debian/test2/usr/share/applications/
install -m 644 -p c:/Users/bcue/Qt/test2/test2.png /c/Users/bcue/Qt/test2/debian/test2/usr/share/icons/hicolor/64x64/apps/
install -m 755 -p "test2" "/c/Users/bcue/Qt/test2/debian/test2/opt/test2/bin/test2"
make[1]: Leaving directory `/c/Users/bcue/Qt/test2'
sed 's:^Icon=.*:Icon=/usr/share/icons/hicolor/64x64/apps/test2.png:' /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop > /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed || echo -n
mv /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop || echo -n
sed 's:Exec=.*:Exec=/opt/test2/bin/test2:' /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop > /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed || echo -n
mv /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop.sed /C/Users/bcue/Qt/test2/debian/test2/usr/share/applications/test2.desktop || echo -n
dh_testdir
dh_testroot
dh_installchangelogs
dh_installdocs
dh_installexamples
dh_installman
dh_link
dh_strip
dh_compress
dh_fixperms
dh_installdeb
dh_shlibdeps
dh_gencontrol
dpkg-shlibdeps: warning: dependency on libgcc_s.so.1 could be avoided if "debian/test2/opt/test2/bin/test2" were not uselessly linked against it (they use none of its symbols).
dpkg-shlibdeps: warning: dependency on libmdeclarativecache.so.0 could be avoided if "debian/test2/opt/test2/bin/test2" were not uselessly linked against it (they use none of its symbols).
dpkg-shlibdeps: warning: dependency on libpthread.so.0 could be avoided if "debian/test2/opt/test2/bin/test2" were not uselessly linked against it (they use none of its symbols).
dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends}
dh_md5sums
dh_builddeb
a - debian-binary
a - control.tar.gz
a - data.tar.gz
dpkg-buildpackage: binary only upload (no source included)
Use of uninitialized value in undef operator at /madbin/dpkg-buildpackage line 369.
dpkg-genchanges -b -u.. >../test2_0.0.1_armel.changes
dpkg-genchanges: binary-only upload - not including any source code
Package created.
Installing package to sysroot ...
c:\Users\bcue\Qt\qt-components-qt-components\C;c:\qtsdk\madde\Users\bcue\Qt\test2\test2_0_0_1_armel.deb: No such file or directory
c:\qtsdk\madde\targets\harmattan-nokia-meego-api\bin\ar.exe:
Cannot find package name (in debian control file).
Connecting to device...
Started uploading file 'C:\Users\bcue\Qt\test2\test2_0_0_1_armel.deb'.
Successfully uploaded file 'C:\Users\bcue\Qt\test2\test2_0_0_1_armel.deb'.
Installing package to device...
warning, in file '/var/lib/dpkg/status' near line 663 package 'mp-harmattan-rm680-pr':
missing description
(Reading database ...
29097 files and directories currently installed.)
Preparing to replace test2 0.0.1 (using .../test2_0_0_1_armel.deb) ...
Unpacking replacement test2 ...
aegis-installing test2 (from 'com.nokia.maemo')
dpkg: dependency problems prevent configuration of test2:
test2 depends on libqt4-declarative (>= 4.7.4~git20110516); however:
Version of libqt4-declarative on system is 4.7.3~git20110329-0maemo1+0m6.
test2 depends on libqtcore4 (>= 4.7.4~git20110516); however:
Version of libqtcore4 on system is 4.7.3~git20110329-0maemo1+0m6.
test2 depends on libqtgui4 (>= 4.7.4~git20110516); however:
Version of libqtgui4 on system is 4.7.3~git20110329-0maemo1+0m6.
dpkg: error processing test2 (--install):
dependency problems - leaving unconfigured
Processing triggers for desktop-file-utils ...
Errors were encountered while processing:
test2
Deployment failed.
Error while building project test2 (target: Harmattan)
When executing build step 'Deploy to Harmattan device'
did you updated your Qt Creator? (2.3.1 if I'm not wrong)
the update bring along the updated SDK for the meego harmattan,.
in that case you should also update your meego phone too because there's some dependency for the newest library. (read the error, dependency-problem)
check here for the update package
http://www.developer.nokia.com/search/search.xhtml?view=ebs&hv=fn:type%3DfnType:Terminal&s=ft&tl=0&ob=best&me=false&l=20&expandDoc=false&k=N950+device+update&oldK=N950+device+update
this one problem makes me revert my QtCreator to the old one , I'm not allowed to upgrade the phone. duh

Python mySQL PPC Mac install

I am trying to install mySQL for Python on PPC ibook G4 running Leopard. I have Python 2.7.2, XCODE 3.1.3 and MAMP 1.9.6 installed.
I was trying both MySQL-Python-1.2.2 and MySQL-Python-1.2.3, but I am always getting this error:
andreass-ibook-g4:MySQL-python-1.2.3 aed0101$ sudo python setup.py buildrunning build
running build_py
copying MySQLdb/release.py -> build/lib.macosx-10.3-fat-2.7/MySQLdb
running build_ext
building '_mysql' extension
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -isysroot/Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch i386 -g -O2 -DNDEBUG -g -O3 -Dversion_info=(1,2,3,'final',0) -D__version__=1.2.3 -I/Applications/MAMP/Library/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.3-fat-2.7/_mysql.o -fno-omit-frame-pointer -g
_mysql.c:36:23: error: my_config.h: No such file or directory
_mysql.c:38:19: error: mysql.h: No such file or directory
_mysql.c:39:26: error: mysqld_error.h: No such file or directory
...more errors
lipo: can't figure out the architecture type of: /var/tmp//ccM5WtnK.out
error: command 'gcc-4.0' failed with exit status 1
Can anybody help me with this?
Thanks.
It looks like the MySQL development headers are not found. If running mysql_config from the shell gives an error, that's probably why. Make sure mysql_config is on your path or else edit site.cfg and set the correct path in there. Normally setup.py will bail out if mysql_config exits with an error, so it's not clear what happened here.

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