I followed this tutorial for installing cx_oracle on Mac. After some tweaks it was successful. I was using Mavericks earlier. Then I got an upgrade to El Capitan. That's where the disaster came in.
It stopped working. I couldn't find related files in the directory earlier. Due to System Integrity Protection, I go through the whole process again and installed this at usr/local/lib/share/oracle/installclient_11_2.
But now when I run the program. It throws this error message:
ImportError: dlopen(/Library/Python/2.7/site-packages/cx_Oracle.so, 2): Library not loaded: /ade/b/3071542110/oracle/rdbms/lib/libclntsh.dylib.11.1
Referenced from: /Library/Python/2.7/site-packages/cx_Oracle.so
Reason: image not found
I tried a lot of solutions online, like https://gist.github.com/rmoff/5a70862f27d2284e9541, http://kevindalias.com/2014/03/26/how-to-set-up-cx_oracle-for-python-on-mac-os-x-10-89/
Still no luck on me:(
Any suggestions are welcome. Thanks in advance!
==========================================================================
UPDATE:
Found this post online, works magically on El Capitan. Delete the old install, start fresh following this intruction step-by-step.
This is related to the system integrity protection (SIP) changes in El Capitan, which among other things prevents DYLD_LIBRARY_PATH being inherited by spawned processes.
You can modify the cx_Oracle.so library to use the actual path to the Oracle client library instead of the searched path that no longer works; make sure you have ORACLE_HOME still set to point to your actual instant client location, and also note that the exact path reported by ImportError should be used - the 3071542110 value may vary depending on the version/build of Instant Client you have installed:
export ORACLE_HOME=/usr/local/lib/share/oracle/installclient_11_2
install_name_tool -change \
/ade/b/3071542110/oracle/rdbms/lib/libclntsh.dylib.11.1 \
$ORACLE_HOME/libclntsh.dylib.11.1 \
/Library/Python/2.7/site-packages/cx_Oracle.so
... but then that library can't find another Oracle one:
ImportError: dlopen(/Library/Python/2.7/site-packages/cx_Oracle.so, 2): Library not loaded: /ade/b/3071542110/oracle/ldap/lib/libnnz11.dylib
Referenced from: /usr/local/lib/share/oracle/installclient_11_2/libclntsh.dylib.11.1
Reason: image not found
So you'd need to change that library too, which you may be less comfortable with:
install_name_tool -change \
/ade/b/3071542110/oracle/ldap/lib/libnnz11.dylib \
$ORACLE_HOME/libnnz11.dylib \
$ORACLE_HOME/libclntsh.dylib.11.1
Depending on the exact client version/build you may need to make the file writable before running that command, with:
chmod 755 $ORACLE_HOME/libclntsh.dylib.11.1
With those changes I can run the cx_Oracle tests on El Capitan.
More into on install_name_change here.
It looks like the 12c instant client has been built in a way that avoids this issue, so upgrading to that is gong to be simpler than hacking around int he 11g files.
sample fix with
ln -s /opt/oracle/product/12.1.0/instantclient_12_1/libclntsh.dylib.12.1 /usr/local/lib/libclntsh.dylib.12.1
Related
I was going through the Flow installation and when I typed sumo --version into the terminal I got the following error message:
dyld: Library not loaded: /usr/local/opt/proj/lib/libproj.13.dylib
Referenced from: /Users/apple/sumo_binaries/bin/sumo
Reason: image not found
I've tried reinstalling sumo but the problem persisted.
How can I solve this issue?
I've found a fix for the problem.
Type the following into the terminal:
ln -s /usr/local/opt/proj/lib/libproj.15.dylib /usr/local/opt/proj/lib/libproj.13.dylib
Open up the directory mentioned above and make sure both libraries show (even if one of them is a shortcut) and rerun the sumo installation.
Note: you may have to change the paths depending on where your libproj.15.dylib is located.
I am currently trying - unsuccessfully to install perl PDL as I would like to automate some of my data analysis and graphics generation.
Unfortunately I seem unable to even install the necessary modules without issue, let alone create a small script to deal with my data files.
I have some rudementary experience with Perl but Nothing fancy and am using Windows 10 x64.
Initially I went for the x64 strawberry perl v5.24 installation, followed by ppm installations of Astro::FITS::Header, Convert::UU, OpenGL and PDL - as instructed here http://pdl.perl.org/?page=install. However, there were issues with the installation of Inline::C and after trying the example listed on page 5 of the PDL_Book_Latest http://sourceforge.net/projects/pdl/files/PDL/2.4.10/PDL-Book-20120205.pdf/download there wasn't any image appearing, nor image file in any location I could think to search. Back to Google and still no luck finding any information on the source of this issue so I decided to go back to square one and use an older version in the hopes that it would be more well documented.
So, uninstallation of strawberry perl through Windows installed programs dialog, deletion of strawberry folder and registry entries containing "strawberry". Then a new installation of perl, with the Padre IDE, v5.14 - maybe some debugging fonctionality will help pinpoint the errors. Started installing the same modules (Astro::FITS::Header, Convert::UU, OpenGL, PGPLOT). Astro and Convert worked fine, but the OpenGL started throwing errors about ExtUtils::F77 which I am apparently missing after a few more hours searching. I go to install this module and it keeps giving errors about 'gfortan' being an unknown command... It was my understanding that the idea of PDL was to avoid fortran and C, and I have found next to no information about this installation problem so far.
So i decided to try an alternative approach. I installed the ppm module from cpan and repeated the initial installation process through the ppm command. This time i get:
"Unknown element 'PROVIDE' found inside SOFTPKG. at C:/Dwimperl/perl/site/lib/PPM.pm line 1462."
So my question is as follows:
Am I missing some critical step in the installation process? Is my system just handing this really badly, and if so is there any sort of possible work around? Is the fact that I tried two different versions liable to create path issues that could be at the root of this problem?
Could anyone provide an alternative and preferably not too complex route to install PDL with a given perl installation on Windows 10?
EDIT 1:
Here is the code for the error I got trying to install Inline::C, an apparent pre-requisite for PDL
code deleted to make space for updates...
EDIT 3:
I reinstalled GnuWin32 in the directory specified by PATH, rather that changing PATH, and the tried the installation again. Inline::C gave the same 'diff' and 'rm' errors. So i ran "cpanm --notest 'package'" to install Inline::C and then PDL, both said they were successful. However, even using '--notest' cpanm could not install OpenGL and PGPLOT.
The final objectif is to be able to produce graphics using the fonctions from PGPLOT: for example
# use PDL;
# use PDL::Graphics::PGPLOT;
# imag(sin(rvals(200,200)+1));
yet this doesn't work of course if PGPLOT can't install.
EDIT 4:
Tried the fix found by #Dr.Avalange at sourceforge https://sourceforge.net/p/pogl/bugs/26/ and noticed that I seem to have multiple copies of this file.
Here
Is this normal...?
EDIT 5:
So i uninstalled perl, deleted any lingering files I could find in %APPDATA%, %USERPROFILE% and C:/DWIM, and then ran ccleaner just in case I missed anything.
I then downloaded Strawberry perl 5.24.1 x64 for Windows and installed it.
After this, I ran 'cpanm Astro::FITS::Header', cpanm 'Convert-UU' and 'cpanm OpenGL' as per http://pdl.perl.org/?page=install. This all worked fine. Then I ran 'cpanm PDL' which installed Inline, Pegex, Win32::Mutex and Module::Compile dependencies. However, if had the same error with Inline::C that you mentioned previously.
I already had GetGnuWin32 installed before so not sure why this isn't working. The Windows 'Path' environment (not PATH - this doesn't exist according to the advaced system dialogue) is noted as
%USERPROFILE%\AppData\Local\Microsoft\WindowsApps;
In this directory I have the folder GetGnuWin32 which should have installed all the packages from the link you provided, unless there is a supplementary step that I missed to install this correctly? So I redownloaded the DiffUtils setup and ran that, installing to \programfiles(x86) (default option). I then reran 'cpanm PDL'.
I still get the same 'diff' error message. So is DiffUtils, not installing properly? (I did close and re-open the commandline between tries and after the installation)
EDIT 6:
So after installing PDL and PGPLOT with --notest I tried to run the following test and it failed. See below
C:\Windows\system32>perldl
perlDL shell v1.357
PDL comes with ABSOLUTELY NO WARRANTY. For details, see the file
'COPYING' in the PDL distribution. This is free software and you
are welcome to redistribute it under certain conditions, see
the same file for details.
ReadLines, NiceSlice, MultiLines enabled
Reading PDL/default.pdl...
Found docs database C:/Strawberry/perl/site/lib/PDL/pdldoc.db
Type 'help' for online help
Type 'demo' for online demos
Loaded PDL v2.017 (supports bad values)
Note: AutoLoader not enabled ('use PDL::AutoLoader' recommended)
pdl> use PDL::Graphics//PLplot
Unknown regexp modifier "/P" at (eval 62) line 4, at end of line
Unknown regexp modifier "/L" at (eval 62) line 4, at end of line
Unknown regexp modifier "/t" at (eval 62) line 4, at end of line
BEGIN not safe after errors--compilation aborted at (eval 62) line 5, <DATA> line 207.
pdl> use PDL::Graphics::PLplot
Can't locate PDL/Graphics/PLplot.pm in #INC (you may need to install the PDL::Graphics::PLplot module) (#INC contains: C:/Strawberry/perl/site/lib/MSWin32-x64-multi-thread C:/Strawberry/perl/site/lib C:/Strawberry/perl/vendor/lib C:/Strawberry/perl/lib .) at (eval 72) line 5.
BEGIN failed--compilation aborted
pdl> use PDL
pdl> use lib 'C:/Strawberry/perl/site/lib/PDL/Graphics'
pdl> use PGPLOT
pdl> use PDL::Graphics::PGPLOT
pdl> imag(sin(rvals(200,200)+1))
Undefined subroutine &PDL::Graphics::PGPLOT::pgqinf called at C:/Strawberry/perl/site/lib/PDL/Graphics/PGPLOT.pm line 408, <DATA> line 90.
pdl> exit
C:\Windows\system32>cpanm PDL::Graphics::PGPLOT::pgqinf
! Finding PDL::Graphics::PGPLOT::pgqinf on cpanmetadb failed.
! Finding PDL::Graphics::PGPLOT::pgqinf () on mirror http://www.cpan.org failed.
! Couldn't find module or a distribution PDL::Graphics::PGPLOT::pgqinf
C:\Windows\system32>cpan PDL::Graphics::PGPLOT::pgqinf
Loading internal null logger. Install Log::Log4perl for logging messages
CPAN: CPAN::SQLite loaded ok (v0.211)
Database was generated on Thu, 13 Apr 2017 13:49:14 GMT
C:\Windows\system32>
There was already a directory problem but I managed to point it in th right direction I had thought. Also tried installing the PLplot 'cpanm' said the installation was successful but there is no .pm file, only a .pd in another directory and so the use PDL::Graphics::PLplot fails as there is no .pm file to find.
EDIT: 7
So retrying ppm install http://www.sisyphusion.tk/ppm/PGPLOT.ppd seemed to work this time as the links int he explanation you provided are no longer in use
http://www.kalinabears.com.au/w32perl/pgplot-5.2.2-mingw32.tar.bz2
http://jrfonseca.home.dyndns.org/projects/gnu-win32/software/ported/patches/pgplot-5.2.2-mingw32.diff.gz
And while this seemed to work, there are no traces of the files that were listed as necessary for the installation, unless they were just for this specific method?
pgplot/bin/cpgplot.dll
pgplot/bin/pgplot.dll
pgplot/bin/grfont.dat
pgplot/include/cpgplot.h
pgplot/lib/cpgplot.a
pgplot/lib/pgplot.a
finally, trying the example again gives the following; no errors, but no image either...
Microsoft Windows [version 10.0.14393]
(c) 2016 Microsoft Corporation. Tous droits réservés.
C:\Windows\system32>perldl
perlDL shell v1.357
PDL comes with ABSOLUTELY NO WARRANTY. For details, see the file
'COPYING' in the PDL distribution. This is free software and you
are welcome to redistribute it under certain conditions, see
the same file for details.
ReadLines, NiceSlice, MultiLines enabled
Reading PDL/default.pdl...
Found docs database C:/Strawberry/perl/site/lib/PDL/pdldoc.db
Type 'help' for online help
Type 'demo' for online demos
Loaded PDL v2.017 (supports bad values)
Note: AutoLoader not enabled ('use PDL::AutoLoader' recommended)
pdl> use PDL
pdl> use PDL::Graphics::PGPLOT
pdl> imag(rvals(200,200)+1)
%PGPLOT, Unable to read font file: grfont.dat
%PGPLOT, Use environment variable PGPLOT_FONT to specify the location of the PGPLOT grfont.dat file.
Displaying 200 x 200 image from 1 to 142.421356201172, using 240 colors (16-255)...
pdl> $ENV{PGPLOT_FONT} = "C:/Strawberry/perl/site/lib/PGPLOT/pgplot_supp"
pdl> imag(rvals(200,200)+1)
Displaying 200 x 200 image from 1 to 142.421356201172, using 240 colors (16-255)...
pdl>
After translating from French I can see that you don't have diff in your system. Either install diff (part of gnu32: http://gnuwin32.sourceforge.net/) or just skip the tests. See also:
https://github.com/ingydotnet/inline-c-pm/issues/60
With Strawberry 5.24.1 simply type the following from the command prompt:
cpanm --notest PDL
or if you want to watch everything that's going on:
cpanm -v --notest PDL
This will take some time to run.
I built my pass on Linux and it worked there correctly. Now when I brought in my code to Mac OS X 10.9 on Mac Airbook, its not working anymore. I am describing below the steps I took for building my llvm pass.
My source tree is llvm-3.4 and llv-3.4/tools/clang-3.4
I ran ./configure --prefix=/some-path --enable-targets=host which was successful.
Then I ran make && make install which completed without any errors.
I exported the bin path export PATH=/some-path/bin:$path and checked for which clang which opt and they pointed to my installation.
Now when I tried to load hello pass opt -load /some-path/lib/LLVMHello.dylib -hello <fac.bc >/dev/null I get the following error
Error opening '/some-path/lib/LLVMHello.dylib': dlopen(/some-path/lib/LLVMHello.dylib, 9): Symbol not found: __ZN4llvm12FunctionPass17assignPassManagerERNS_7PMStackENS_15PassManagerTypeE
Referenced from: /some-path/lib/LLVMHello.dylib
Expected in: flat namespace
in /some-path/lib/LLVMHello.dylib
-load request ignored.
opt: Unknown command line argument '-hello'. Try: '/some-path/bin/opt -help'
opt: Did you mean '-help'?
Can someone help me fix this issue or at least point in the right direction.
In my case, the dynamic LLVM library, which is required for dynamically loaded passes, was missing. I solved it by configuring LLVM with --enable-shared. I also had --enable-keep-symbols set, but I don't think this is necessary. The full configure command I used:
./configure --enable-shared --enable-keep-symbols
I know I'm a bit late with the answer, but I recently ran into the same problem. And since I spent quite some time solving the issue, I wanted to pass on my findings. Hope it helps.
Cheers, Marcus
I am attempting to install the Cairo package in the development version of R on Mac OS X 10.7.4, but I'm running into an issue that I cannot resolve.
I have installed Cairo with homebrew (i.e., brew install cairo) and received the following message:
==> Caveats This formula is keg-only, so it was not symlinked into /usr/local.
Mac OS X already provides this program and installing another version
in parallel can cause all kinds of trouble.
The Cairo provided by Leopard is too old for newer software to link
against.
Generally there are no consequences of this for you. If you build your
own software and it requires this formula, you'll need to add its lib
& include paths to your build variables:
LDFLAGS -L/usr/local/Cellar/cairo/1.12.2/lib
CPPFLAGS -I/usr/local/Cellar/cairo/1.12.2/include
With the above message in mind, I attempted to install the Cairo package from R-Forge with the following R command:
install.packages("Cairo", repos="http://www.rforge.net/", configure.args = c("CAIRO_LIBS=/usr/local/Cellar/cairo/1.12.2/lib", "CAIRO_CFLAGS=/usr/local/Cellar/cairo/1.12.2/include/cairo"))
I receive the following error:
checking cairo.h usability... no
checking cairo.h presence... no
checking for cairo.h... no
configure: error: Cannot find cairo.h!
Please install cairo (http://www.cairographics.org/) and/or set
CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package ‘Cairo’
I repeated the same command without the repos argument (by default, I use the FHCRC mirror) with the same result.
At this point, the problem seems obvious: the file cairo.h is not present. But then I listed the files in the include/cairo directory. Here's the response:
ls /usr/local/Cellar/cairo/1.12.2/include/cairo
cairo-deprecated.h cairo-ft.h
cairo-ps.h
cairo-script-interpreter.h
cairo-svg.h
cairo-xcb.h
cairo-xlib.h
cairo-features.h
cairo-pdf.h
cairo-quartz.h
cairo-script.h
cairo-version.h
cairo-xlib-xrender.h
cairo.h
So, I'm pointing the installation of the Cairo package to the appropriate place, but the error persists. I have tried variations, such as CAIRO_CFLAGS=/usr/local/Cellar/cairo/1.12.2/include, with no luck.
Thoughts? Any help you can provide is greatly appreciated.
In case it's necessary, here is my sessionInfo:
R Under development (unstable) (2012-08-08 r60208) Platform: x86_64-apple-darwin11.4.0 (64-bit)
locale: [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] BiocInstaller_1.5.12
loaded via a namespace (and not attached): [1] tools_2.16.0
I had similar issue with cairo config error, and I already installed cairo with homebrew. Try below
brew install pkg-config
This solved mine problem.
A coworker and I just fixed the problem by ignoring all of what I typed above. Rather, we installed Cairo and all of its dependencies from source manually, thereby bypassing the usage of brew or variants like port. This worked like a charm, so I am not entirely sure what was wrong above.
After trying everything listed here, I found this blog post about installing the "full R package" using brew: https://luispuerto.net/blog/2018/05/11/installing-r-with-homebrew-with-all-the-capabilities/
What finally worked for me was building R explicitly with cairo (brew's default R tap uses --without-cairo and simply editing the tap did not solve the issue for me).
Works like a charm for me with R 4.0.2, cairo 1.16.0_3 under macOS Catalina 10.15.6.
This has been driving me crazy for 2 days.
I have been trying to install psycopg2 using easy_install and no matter what I try (i.e using gcc-4.0 instead of the snow leopard default one) I always get the same error:
error: Setup script exited with error: command '/usr/bin/gcc-4.0' failed with exit status 1
Please see: http://dpaste.com/hold/228252/
I have googled that error so many times and nothing I have found seem to help.
Looks like you're missing a dependency, the development files for libpq. The relevant log part is here:
In file included from psycopg/psycopgmodule.c:32In file included from psycopg/psycopgmodule.c:32:
./psycopg/psycopg.h:31:22: error: libpq-fe.h: No such file or directory
Try installing libpq development files and then rerun easy_install. You may hit another missing dependency; pay attention to the first error that GCC spits out.
Link http://dpaste.com/hold/228252/ seems to be dead, this is how I solved this problem (Mac OS X 10.6, virtualenv).
If pip fails with this message, just take a look to build folder in your virtual environment. You should edit setup.cfg file there, particularly include_dirs and library_dirs. In first one set your include folders, my option was:
include_dirs=/opt/local/include/postgresql84:/opt/local/include/postgresql84/server
and most likely you will need to set library_dirs to correct location as well:
library_dirs=/opt/local/lib/postgresql84.
probably you should install postgresql-devel first
yum -y install postgresql-devel