It appears as if you are missing the following file:
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch
Can you look to see what *patch files you have in this
directory? And did you download the source tar archive or did
you check out the code from the sourceforge svn repository?
-Joe
On Thu, May 28, 2015 at 10:38 AM, MD <md.is...@students.mq.edu.au
<mailto:md.is...@students.mq.edu.au>> wrote:
Hi Joe,
I am trying to install 4.8 on linux and getting the following
error. I also tried 4.71 , and both on ubuntu 12.04 and
14.04. . Can you please help?
tu-x86_64 ZLIB_INCL="" ZLIB_LIB=-lz STATIC_LIBSTDCPP=
make[1]: Entering directory
`/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/extern/gzstream'
g++ -I. -O -c -o Ubuntu-x86_64gzstream.o gzstream.cpp
ar cr
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/libgzstream.a
Ubuntu-x86_64gzstream.o
make[1]: Leaving directory
`/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/extern/gzstream'
uncompressing HDF5 library
mkdir -p
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6
cd
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6;
cd ..; tar zxf
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.tar.gz;
\
for P in
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch;
do\
echo "applying HDF5 patch $P";\
patch -s -p0 < $P;\
done
applying HDF5 patch
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.gcc47patch
/bin/sh: 4: patch: not found
applying HDF5 patch
/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6.mingwpatch
/bin/sh: 4: patch: not found
make: ***
[/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/hdf5-1.8.6]
Error 127
root@trans-proteomic-pipeline:/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src#
<mailto:root@trans-proteomic-pipeline:/home/ubuntu/software/TPP-4.8.0/trans_proteomic_pipeline/src#>
Thank you
Regards
Mohammad
On Saturday, November 22, 2014 at 9:07:05 AM UTC+11,
jsl...@systemsbiology.org <mailto:jsl...@systemsbiology.org>
wrote:
Announcing the official release of Trans-Proteomic
Pipeline (TPP) 4.8.0 "PHILAE"
We are proud to offer a update to the Trans-Proteomic
Pipeline (TPP) software, release 4.8.0 (4.8 revision).
The software is available for Windows as well as Linux
(and unofficially) through OSX source from all the usual
locations (please see the section below, "Getting the
software"). Most users are recommended to use the
Windows installer, which installs and configures the TPP
and other required software (such as a web server). For
advanced users who need to customize the TPP, or for
those who run on Linux or OS X, you can download the
source code.
== Release Notes ==
* Release notes on the most important new features,
changes, and known issues are available at:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.8.0_Release_Notes
<http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.8.0_Release_Notes>"
== Getting the TPP Software ==
* Download the TPP version 4.8.0 native windows installer
from the Sashimi SourceForge project file release page:
"http://sourceforge.net/
<http://goog_2056063534>http://sourceforge.net/projects/sashimi/files/Trans-Proteomic
Pipeline (TPP)
<http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29>"
* Everyone is encouraged to read and contribute to our
wiki, at
"http://tools.proteomecenter.org/wiki/";
* For guides to installing and using our software, please
see our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
<http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP>"
* For downloading the source code, please go to the
following link:
"http://sourceforge.net/projects/sashimi/files/"; and
find the 4.8.0 source code .zip package;
or, check out the code directly from svn:
"svn co
svn://svn.code.sf.net/p/sashimi/code/tags/release_4-8-
<http://svn.code.sf.net/p/sashimi/code/tags/release_4-8->0"
For building from source, please refer to the README and
INSTALL files in src/ directory of TPP as well as the wiki.
== Acknowledgements ==
The TPP Team: Luis, David, Mike, and Joe, plus all other
developers who contributed to this release from the ISB.
Thanks to developers and users from the TPP's user
community who also provide feedback and code contributions.
--
Joe Slagel
Institute for Systems Biology
jsla...@systemsbiology.org
<mailto:jsla...@systemsbiology.org>
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