Hi,
I'm sorry I cannot reproduce this.
Here's my Directory Structure -- I tend to keep the patches with the
easyconfig and not with the sources since different patches might be needed
for the same "sourceball" depending on which easyconfig you want to build
(which also is what what easybuild does, I presume for the same reason):
*easyconfigs/Bridger*
*├── Bridger-r2014-12-01-fix-plugin-Makefiles.patch*
*└── Bridger-r2014-12-01-foss-2015a.eb*
Here's the log lines (with -d and the patch line in bold near the bottom)):
*# eb --force --pretend Bridger/Bridger-r2014-12-01-foss-2015a.eb -s patch
-d*
*...*
*== 2015-10-12 10:00:18,816 main.MakeCp INFO patching...*
*== 2015-10-12 10:00:18,816 main.MakeCp INFO Starting patch step*
*== 2015-10-12 10:00:18,819 main.easyconfig.templates DEBUG config:
{'preinstallopts': ['', 'Extra prefix options for installation.', (3,
'build')], 'configure*
*_cmd_prefix': ['', 'Prefix to be glued before ./configure', (1,
'easyblock-specific')], 'postinstallcmds': [[], 'Commands to run after the
install step.', (3,*
* 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts,
unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip
existing softw*
*are', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True)
or backup (False) the previous build directory with identical name or
not.', (4, 'fil*
*e-management')], 'installopts': ['', 'Extra options for installation', (3,
'build')], 'sources': [['%(name)s_%(version)s.tar.gz'], 'List of source
files', (3,*
* 'build')], 'versionsuffix': ['', 'Additional suffix for software version
(placed after toolchain name)', (3, 'build')], 'license_server': [None,
'License ser*
*ver for software', (6, 'license')], 'keeppreviousinstall': [False,
'Boolean to keep the previous installation with identical name. Experts
only!', (4, 'file-m*
*anagement')], 'hiddendependencies': [[], 'List of dependencies available
as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for
sources an*
*d patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine
whether symlinks are to be kept during copying or if the content of the
files pointed*
* to should be copied', (4, 'file-management')], 'cleanupoldinstall':
[True, 'Boolean to remove (True) or backup (False) the previous install
directory with id*
*entical name or not.', (4, 'file-management')], 'builddependencies':
[[{'external_module_metadata': {}, 'dummy': False, 'toolchain': {'version':
'2015a', 'nam*
*e': 'foss'}, 'name': 'Boost', 'short_mod_name':
'Boost/1.58.0-foss-2015a-Python-2.7.9', 'external_module': False,
'versionsuffix': '-Python-2.7.9', 'full_mod_*
*name': 'Boost/1.58.0-foss-2015a-Python-2.7.9', 'version': '1.58.0',
'hidden': False}], 'List of build dependencies', (5, 'dependencies')],
'dontcreateinstalld*
*ir': [False, 'Boolean to create (False) or not create (True) the install
directory', (4, 'file-management')], 'modextravars': [{}, 'Extra
environment variable*
*s to be added to module file', (8, 'modules')], 'unpack_options': ['',
'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name
of the user*
*group for which the software should be available', (6, 'license')],
'versionprefix': ['', 'Additional prefix for software version (placed
before version and t*
*oolchain name)', (3, 'build')], 'with_configure': [True, 'Run configure
script before building', (3, 'build')], 'parsed': [True, 'This is a parsed
easyconfig'*
*, 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build
command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version
this spec-file w*
*as written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3,
'build')], 'start_dir': [None, 'Path to start the make in. If the path is
absolute,*
*use that path. If not, this is added to the guessed path.', (4,
'file-management')], 'version': ['r2014-12-01', 'Version of software', (0,
'mandatory')], 'ext*
*s_filter': [None, 'Extension filter details: template for cmd and input to
cmd (templates for name, version and src).', (7, 'extensions')],
'modaliases': [{},*
* 'Aliases to be defined in module file', (8, 'modules')],
'allow_system_deps': [[], 'Allow listed system dependencies (format:
(<name>, <version>))', (5, 'dep*
*endencies')], 'osdependencies': [[], 'OS dependencies that should be
present on the system', (5, 'dependencies')], 'modluafooter': ['', 'Footer
to include in*
*generated module file (Lua syntax)', (8, 'modules')], 'homepage':
['https://wiki.gacrc.uga.edu/wiki/Bridger
<https://wiki.gacrc.uga.edu/wiki/Bridger>', 'The homepage of the software',
(0, 'mandatory')*
*], 'license_file': [None, 'License file for software', (6, 'license')],
'tests': [[], 'List of test-scripts to run after install. A test script
should return*
*a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra
options passed to make step (default already has -j X)', (3, 'build')],
'tar_config_opts': [False, 'Override tar settings as determined by
configure.', (1, 'easyblock-specific')], 'description': ['Bridger is an
efficient de novo trascriptome assembler for RNA-Seq data. ', 'A short
description of the software', (0, 'mandatory')], 'modextrapaths': [{'PATH':
''}, 'Extra paths to be prepended in module file', (8, 'modules')],
'exts_list': [[], 'List with extensions added to the base installation',
(7, 'extensions')], 'docurls': [None, 'List of urls with documentation of
the software (not necessarily on homepage)', (0, 'mandatory')], 'stop':
['patch', 'Keyword to halt the build process after a certain step.', (3,
'build')], 'exts_classmap': [{}, 'Map of extension name to class for
handling build and installation.', (7, 'extensions')], 'moduleforceunload':
[False, 'Force unload of all modules when loading the extension', (8,
'modules')], 'dependencies': [[{'external_module_metadata': {}, 'dummy':
False, 'toolchain': {'version': '2015a', 'name': 'foss'}, 'name': 'zlib',
'short_mod_name': 'zlib/1.2.8-foss-2015a', 'external_module': False,
'versionsuffix': '', 'full_mod_name': 'zlib/1.2.8-foss-2015a', 'version':
'1.2.8', 'hidden': False}, {'external_module_metadata': {}, 'dummy': False,
'toolchain': {'version': '2015a', 'name': 'foss'}, 'name': 'Boost',
'short_mod_name': 'Boost/1.58.0-foss-2015a-Python-2.7.9',
'external_module': False, 'versionsuffix': '-Python-2.7.9',
'full_mod_name': 'Boost/1.58.0-foss-2015a-Python-2.7.9', 'version':
'1.58.0', 'hidden': False}, {'external_module_metadata': {}, 'dummy':
False, 'toolchain': {'version': '2015a', 'name': 'foss'}, 'name': 'Perl',
'short_mod_name': 'Perl/5.20.1-foss-2015a-bare', 'external_module': False,
'versionsuffix': '-bare', 'full_mod_name': 'Perl/5.20.1-foss-2015a-bare',
'version': '5.20.1', 'hidden': False}], 'List of dependencies', (5,
'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this
software', (8, 'modules')], 'key': [None, 'Key for installing software',
(6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH
exextensions specified by module naming scheme.', (8, 'modules')],
'prefix_opt': ['--prefix=', 'Prefix command line option for configure
script', (1, 'easyblock-specific')], 'modloadmsg': [{}, 'Message that
should be printed when generated module is loaded', (8, 'modules')],
'modtclfooter': ['', 'Footer to include in generated module file (Tcl
syntax)', (8, 'modules')], 'parallel': [24, 'Degree of parallelism for e.g.
make (default: based on the number of cores, active cpuset and restrictions
in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build
(True) or not build (False) in the installation directory', (4,
'file-management')], 'patches':
[['%(name)s-%(version)s-fix-plugin-Makefiles.patch'], 'List of patches to
apply', (3, 'build')], 'sanity_check_paths': [{'dirs': ['bin/'], 'files':
['Bridger.pl']}, "List of files and directories to check (format:
{'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': [None,
'Indicates if a test should be run after make; should specify argument
after make (for e.g.,"test" for make test)', (3, 'build')], 'onlytcmod':
[False, 'Boolean/string to indicate if the toolchain should only load the
environment with module (True) or also set all other variables (False) like
compiler CC etc (if string: comma separated list of variables that will be
ignored).', (2, 'toolchain')], 'buildstats': [None, 'A list of dicts with
build statistics', (9, 'other')], 'unwanted_env_vars': [[], "List of
environment variables that shouldn't be set during build", (3, 'build')],
'name': ['Bridger', 'Name of software', (0, 'mandatory')], 'maxparallel':
[None, 'Max degree of parallelism', (3, 'build')], 'toolchain':
[{'version': '2015a', 'name': 'foss'}, 'Name and version of toolchain', (0,
'mandatory')], 'preconfigopts': ['export BOOST_ROOT=$EBROOTBOOST;export
BOOST_INCLUDEDIR=$EBROOTBOOST/include;export
BOOST_LIBRARYDIR=$EBROOTBOOST/lib;export LDFLAGS="-L$EBROOTZLIB/lib -lz
-L$BOOST_LIBRARYDIR";export CFLAGS="-L$EBROOTZLIB/lib -I$EBROOTZLIB/include
-lz -I$BOOST_INCLUDEDIR";', 'Extra options pre-passed to configure.', (3,
'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g.
[('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3,
'build')], 'license_server_port': [None, 'Port for license server', (6,
'license')], 'exts_defaultclass': [None, 'List of module for and name of
the default extension class', (7, 'extensions')], 'source_urls':
[['http://downloads.sourceforge.net/project/rnaseqassembly'
<http://downloads.sourceforge.net/project/rnaseqassembly'>], 'List of URLs
for source files', (3, 'build')], 'easyblock': ['MakeCp', 'EasyBlock to use
for building; if set to None, an easyblock is selected based on the
software name', (3, 'build')], 'toolchainopts': [None, 'Extra options for
compilers', (2, 'toolchain')], 'software_license': [None, 'Software
license', (0, 'mandatory')], 'files_to_copy': [['Bridger.pl',
(['src/get_reads_from_graph'], 'bin/'), (['src/PathSearch'], 'bin/'),
(['src/Assemble'], 'bin/')], 'List of files or dirs to copy', (0,
'mandatory')], 'configopts': ['--with-boost=$BOOST_ROOT', 'Extra options
passed to configure (default already has --prefix)', (3, 'build')],
'software_license_urls': [None, 'List of software license locations', (0,
'mandatory')]}*
*== 2015-10-12 10:00:18,821 main.easyconfig.templates DEBUG version found
in easyconfig is r2014-12-01*
*== 2015-10-12 10:00:18,821 main.easyconfig.templates DEBUG version found
in easyconfig is r2014-12-01*
*== 2015-10-12 10:00:18,822 main.easyconfig.templates DEBUG version found
in easyconfig is r2014-12-01*
*== 2015-10-12 10:00:18,822 main.easyconfig.templates DEBUG name: name,
config: Bridger*
*== 2015-10-12 10:00:18,822 main.easyconfig.templates DEBUG name: version,
config: r2014-12-01*
*== 2015-10-12 10:00:18,822 main.easyconfig.templates DEBUG name:
versionsuffix, config:*
*== 2015-10-12 10:00:18,823 main.easyconfig.templates DEBUG name:
versionprefix, config:*
*== 2015-10-12 10:00:18,824 main.easyconfig.templates DEBUG config:
{'preinstallopts': ['', 'Extra prefix options for installation.', (3,
'build')], 'configure_cmd_prefix': ['', 'Prefix to be glued before
./configure', (1, 'easyblock-specific')], 'postinstallcmds': [[], 'Commands
to run after the install step.', (3, 'build')], 'moduleloadnoconflict':
[False, "Don't check for conflicts, unload other versions instead ", (8,
'modules')], 'skip': [False, 'Skip existing software', (3, 'build')],
'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the
previous build directory with identical name or not.', (4,
'file-management')], 'installopts': ['', 'Extra options for installation',
(3, 'build')], 'sources': [['%(name)s_%(version)s.tar.gz'], 'List of source
files', (3, 'build')], 'versionsuffix': ['', 'Additional suffix for
software version (placed after toolchain name)', (3, 'build')],
'license_server': [None, 'License server for software', (6, 'license')],
'keeppreviousinstall': [False, 'Boolean to keep the previous installation
with identical name. Experts only!', (4, 'file-management')],
'hiddendependencies': [[], 'List of dependencies available as hidden
modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources
and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine
whether symlinks are to be kept during copying or if the content of the
files pointed to should be copied', (4, 'file-management')],
'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the
previous install directory with identical name or not.', (4,
'file-management')], 'builddependencies': [[{'external_module_metadata':
{}, 'dummy': False, 'toolchain': {'version': '2015a', 'name': 'foss'},
'name': 'Boost', 'short_mod_name': 'Boost/1.58.0-foss-2015a-Python-2.7.9',
'external_module': False, 'versionsuffix': '-Python-2.7.9',
'full_mod_name': 'Boost/1.58.0-foss-2015a-Python-2.7.9', 'version':
'1.58.0', 'hidden': False}], 'List of build dependencies', (5,
'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create
(False) or not create (True) the install directory', (4,
'file-management')], 'modextravars': [{}, 'Extra environment variables to
be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra
options for unpacking source', (3, 'build')], 'group': [None, 'Name of the
user group for which the software should be available', (6, 'license')],
'versionprefix': ['', 'Additional prefix for software version (placed
before version and toolchain name)', (3, 'build')], 'with_configure':
[True, 'Run configure script before building', (3, 'build')], 'parsed':
[True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['',
'Extra options pre-passed to build command.', (3, 'build')],
'easybuild_version': [None, 'EasyBuild-version this spec-file was written
for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')],
'start_dir': [None, 'Path to start the make in. If the path is absolute,
use that path. If not, this is added to the guessed path.', (4,
'file-management')], 'version': ['r2014-12-01', 'Version of software', (0,
'mandatory')], 'exts_filter': [None, 'Extension filter details: template
for cmd and input to cmd (templates for name, version and src).', (7,
'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file',
(8, 'modules')], 'allow_system_deps': [[], 'Allow listed system
dependencies (format: (<name>, <version>))', (5, 'dependencies')],
'osdependencies': [[], 'OS dependencies that should be present on the
system', (5, 'dependencies')], 'modluafooter': ['', 'Footer to include in
generated module file (Lua syntax)', (8, 'modules')], 'homepage':
['https://wiki.gacrc.uga.edu/wiki/Bridger
<https://wiki.gacrc.uga.edu/wiki/Bridger>', 'The homepage of the software',
(0, 'mandatory')], 'license_file': [None, 'License file for software', (6,
'license')], 'tests': [[], 'List of test-scripts to run after install. A
test script should return a non-zero exit status to fail', (3, 'build')],
'buildopts': ['', 'Extra options passed to make step (default already has
-j X)', (3, 'build')], 'tar_config_opts': [False, 'Override tar settings as
determined by configure.', (1, 'easyblock-specific')], 'description':
['Bridger is an efficient de novo trascriptome assembler for RNA-Seq data.
', 'A short description of the software', (0, 'mandatory')],
'modextrapaths': [{'PATH': ''}, 'Extra paths to be prepended in module
file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to
the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls
with documentation of the software (not necessarily on homepage)', (0,
'mandatory')], 'stop': ['patch', 'Keyword to halt the build process after a
certain step.', (3, 'build')], 'exts_classmap': [{}, 'Map of extension name
to class for handling build and installation.', (7, 'extensions')],
'moduleforceunload': [False, 'Force unload of all modules when loading the
extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata':
{}, 'dummy': False, 'toolchain': {'version': '2015a', 'name': 'foss'},
'name': 'zlib', 'short_mod_name': 'zlib/1.2.8-foss-2015a',
'external_module': False, 'versionsuffix': '', 'full_mod_name':
'zlib/1.2.8-foss-2015a', 'version': '1.2.8', 'hidden': False},
{'external_module_metadata': {}, 'dummy': False, 'toolchain': {'version':
'2015a', 'name': 'foss'}, 'name': 'Boost', 'short_mod_name':
'Boost/1.58.0-foss-2015a-Python-2.7.9', 'external_module': False,
'versionsuffix': '-Python-2.7.9', 'full_mod_name':
'Boost/1.58.0-foss-2015a-Python-2.7.9', 'version': '1.58.0', 'hidden':
False}, {'external_module_metadata': {}, 'dummy': False, 'toolchain':
{'version': '2015a', 'name': 'foss'}, 'name': 'Perl', 'short_mod_name':
'Perl/5.20.1-foss-2015a-bare', 'external_module': False, 'versionsuffix':
'-bare', 'full_mod_name': 'Perl/5.20.1-foss-2015a-bare', 'version':
'5.20.1', 'hidden': False}], 'List of dependencies', (5, 'dependencies')],
'moduleclass': ['bio', 'Module class to be used for this software', (8,
'modules')], 'key': [None, 'Key for installing software', (6, 'license')],
'include_modpath_extensions': [True, 'Include $MODULEPATH extensions
specified by module naming scheme.', (8, 'modules')], 'prefix_opt':
['--prefix=', 'Prefix command line option for configure script', (1,
'easyblock-specific')], 'modloadmsg': [{}, 'Message that should be printed
when generated module is loaded', (8, 'modules')], 'modtclfooter': ['',
'Footer to include in generated module file (Tcl syntax)', (8, 'modules')],
'parallel': [24, 'Degree of parallelism for e.g. make (default: based on
the number of cores, active cpuset and restrictions in ulimit)', (3,
'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not
build (False) in the installation directory', (4, 'file-management')],
'patches': [['%(name)s-%(version)s-fix-plugin-Makefiles.patch'], 'List of
patches to apply', (3, 'build')], 'sanity_check_paths': [{'dirs': ['bin/'],
'files': ['Bridger.pl']}, "List of files and directories to check (format:
{'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': [None,
'Indicates if a test should be run after make; should specify argument
after make (for e.g.,"test" for make test)', (3, 'build')], 'onlytcmod':
[False, 'Boolean/string to indicate if the toolchain should only load the
environment with module (True) or also set all other variables (False) like
compiler CC etc (if string: comma separated list of variables that will be
ignored).', (2, 'toolchain')], 'buildstats': [None, 'A list of dicts with
build statistics', (9, 'other')], 'unwanted_env_vars': [[], "List of
environment variables that shouldn't be set during build", (3, 'build')],
'name': ['Bridger', 'Name of software', (0, 'mandatory')], 'maxparallel':
[None, 'Max degree of parallelism', (3, 'build')], 'toolchain':
[{'version': '2015a', 'name': 'foss'}, 'Name and version of toolchain', (0,
'mandatory')], 'preconfigopts': ['export BOOST_ROOT=$EBROOTBOOST;export
BOOST_INCLUDEDIR=$EBROOTBOOST/include;export
BOOST_LIBRARYDIR=$EBROOTBOOST/lib;export LDFLAGS="-L$EBROOTZLIB/lib -lz
-L$BOOST_LIBRARYDIR";export CFLAGS="-L$EBROOTZLIB/lib -I$EBROOTZLIB/include
-lz -I$BOOST_INCLUDEDIR";', 'Extra options pre-passed to configure.', (3,
'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g.
[('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3,
'build')], 'license_server_port': [None, 'Port for license server', (6,
'license')], 'exts_defaultclass': [None, 'List of module for and name of
the default extension class', (7, 'extensions')], 'source_urls':
[['http://downloads.sourceforge.net/project/rnaseqassembly'
<http://downloads.sourceforge.net/project/rnaseqassembly'>], 'List of URLs
for source files', (3, 'build')], 'easyblock': ['MakeCp', 'EasyBlock to use
for building; if set to None, an easyblock is selected based on the
software name', (3, 'build')], 'toolchainopts': [None, 'Extra options for
compilers', (2, 'toolchain')], 'software_license': [None, 'Software
license', (0, 'mandatory')], 'files_to_copy': [['Bridger.pl',
(['src/get_reads_from_graph'], 'bin/'), (['src/PathSearch'], 'bin/'),
(['src/Assemble'], 'bin/')], 'List of files or dirs to copy', (0,
'mandatory')], 'configopts': ['--with-boost=$BOOST_ROOT', 'Extra options
passed to configure (default already has --prefix)', (3, 'build')],
'software_license_urls': [None, 'List of software license locations', (0,
'mandatory')]}*
*== 2015-10-12 10:00:18,827 main.easyconfig.templates DEBUG version found
in easyconfig is r2014-12-01*
*== 2015-10-12 10:00:18,827 main.easyconfig.templates DEBUG version found
in easyconfig is r2014-12-01*
*== 2015-10-12 10:00:18,827 main.easyconfig.templates DEBUG version found
in easyconfig is r2014-12-01*
*== 2015-10-12 10:00:18,827 main.easyconfig.templates DEBUG name: name,
config: Bridger*
*== 2015-10-12 10:00:18,828 main.easyconfig.templates DEBUG name: version,
config: r2014-12-01*
*== 2015-10-12 10:00:18,828 main.easyconfig.templates DEBUG name:
versionsuffix, config:*
*== 2015-10-12 10:00:18,828 main.easyconfig.templates DEBUG name:
versionprefix, config:*
*== 2015-10-12 10:00:18,828 main.MakeCp INFO Running method patch_step part
of step patch*
*== 2015-10-12 10:00:18,829 main.MakeCp INFO Applying patch
Bridger-r2014-12-01-fix-plugin-Makefiles.patch*
*== 2015-10-12 10:00:18,829 main.MakeCp DEBUG Source index: 0; patch level:
None; source path suffix: ; copy patch: <module 'copy' from
'/usr/lib64/python2.6/copy.pyc'>*
*== 2015-10-12 10:00:18,829 main.MakeCp DEBUG Determine begin path for
patch Bridger-r2014-12-01-fix-plugin-Makefiles.patch:
/dev/shm/Bridger/r2014-12-01/foss-2015a/Bridger_r2014-12-01*
*== 2015-10-12 10:00:18,829 main.MakeCp DEBUG Applying patch {'path':
'/net/home/marcherm/easyconfigs/Bridger/Bridger-r2014-12-01-fix-plugin-Makefiles.patch',
'md5': 'ce5526c0d21186fb37b07569d3992854', 'name':
'Bridger-r2014-12-01-fix-plugin-Makefiles.patch', 'checksum': None} in path
/dev/shm/Bridger/r2014-12-01/foss-2015a/Bridger_r2014-12-01*
*== 2015-10-12 10:00:18,835 main.filetools DEBUG Guessed patch level 1 for
patch
/net/home/marcherm/easyconfigs/Bridger/Bridger-r2014-12-01-fix-plugin-Makefiles.patch*
*== 2015-10-12 10:00:18,835 main.filetools DEBUG Changing to directory
/dev/shm/Bridger/r2014-12-01/foss-2015a/Bridger_r2014-12-01*
*== 2015-10-12 10:00:18,836 main.run DEBUG run_cmd: running cmd patch -b
-p1 -i
/net/home/marcherm/easyconfigs/Bridger/Bridger-r2014-12-01-fix-plugin-Makefiles.patch
(in /dev/shm/Bridger/r2014-12-01/foss-2015a/Bridger_r2014-12-01)*
*== 2015-10-12 10:00:18,887 main.run DEBUG cmd "patch -b -p1 -i
/net/home/marcherm/easyconfigs/Bridger/Bridger-r2014-12-01-fix-plugin-Makefiles.patch"
exited with exitcode 0 and output:*
*patching file plugins/fastool/Makefile*
*patching file plugins/rsem/makefile*
*patching file plugins/rsem/sam/Makefile*
*patching file plugins/rsem/sam/bcftools/Makefile*
*patching file plugins/rsem/sam/misc/Makefile*
*== 2015-10-12 10:00:18,888 main.run DEBUG Using default regular
expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)*
*== 2015-10-12 10:00:18,888 main.MakeCp INFO Stopping after patch step.*
*== 2015-10-12 10:00:18,889 main.MakeCp INFO Closing log for application
name Bridger version r2014-12-01*
On Thursday, 8 October 2015, Niek de Klein <[email protected]> wrote:
> Hi Martin,
>
>
> Thanks for making the .eb file. However, I am getting the below error for
> the plugin patch, do you know how to fix this?
>
> Thanks,
> Niek
>
> == 2015-10-08 21:23:25,613 main ERROR cmd "patch -b -p1 -i
> /apps/sources/EasyBuild/custom/Bridger-r2014-12-01-fix-plugin-Makefiles.patch"
> exited with exitcode 1 and output:
> patching file plugins/fastool/Makefile
> Hunk #1 FAILED at 1.
> 1 out of 1 hunk FAILED -- saving rejects to file
> plugins/fastool/Makefile.rej
> patching file plugins/rsem/makefile
> Hunk #2 FAILED at 50.
> Hunk #3 FAILED at 83.
> Hunk #4 FAILED at 93.
> Hunk #5 FAILED at 127.
> 4 out of 5 hunks FAILED -- saving rejects to file plugins/rsem/makefile.rej
> patching file plugins/rsem/sam/Makefile
> Hunk #1 FAILED at 1.
> Hunk #2 FAILED at 25.
> Hunk #3 FAILED at 48.
> 3 out of 3 hunks FAILED -- saving rejects to file
> plugins/rsem/sam/Makefile.rej
> patching file plugins/rsem/sam/bcftools/Makefile
> Hunk #1 FAILED at 1.
> Hunk #2 FAILED at 11.
> Hunk #3 FAILED at 31.
> 3 out of 3 hunks FAILED -- saving rejects to file
> plugins/rsem/sam/bcftools/Makefile.rej
> patching file plugins/rsem/sam/misc/Makefile
> Hunk #1 FAILED at 1.
> Hunk #2 FAILED at 11.
> Hunk #3 FAILED at 20.
> Hunk #4 FAILED at 28.
> 4 out of 4 hunks FAILED -- saving rejects to file
> plugins/rsem/sam/misc/Makefile.rej
> (at easybuild/tools/run.py:359 in parse_cmd_output)
> == 2015-10-08 21:23:25,647 main.easyblock WARNING build failed (first 300
> chars): cmd "patch -b -p1 -i
> /apps/sources/EasyBuild/custom/Bridger-r2014-12-01-fix-plugin-Makefiles.patch"
> exited with exitcode 1 and output:
> patching file plugins/fastool/Makefile
> Hunk #1 FAILED at 1.
> 1 out of 1 hunk FAILED -- saving rejects to file
> plugins/fastool/Makefile.rej
> patching file plugins/rsem/
> == 2015-10-08 21:23:25,647 main.MakeCp INFO Closing log for application
> name Bridger version r2014-12-01
>
> On Thu, Oct 8, 2015 at 5:49 PM, Martin <[email protected]> wrote:
>
>> The software derives stuff from BOOST_ROOT existing as an environment
>> variable
>>
>> Anyhow I put some work into it as we also needed Bridger, sorry for it
>> not being a pull request but maybe it is of some use to Niek de Klein.
>>
>> Mind you: Not my best piece of work, but it gets the job done. Also Kudos
>> to Arnau for beating me to it :)
>>
>> best,
>> Martin
>>
>>
>> Files are attached
>> On Wed, Oct 7, 2015 at 5:11 PM, Kenneth Hoste <[email protected]>
>> wrote:
>>
>>> Why the $BOOST_ROOT, and not just use
>>> --configopts="--with-boost=$EBROOTBOOST" ?
>>>
>>
>>
>>
>>
>> --
>> http://www.xing.com/profile/Martin_Marcher
>> http://www.linkedin.com/in/martinmarcher
>> Mobil: +43 / 660 / 62 45 103
>> UID: ATU68801424
>>
>
>
