------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/metis-5.1.0_8.txz ===== Message from metis-5.1.0_8: -- ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/tbb-2020.3.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_3,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.10,1.txz Installing /packages/All/suitesparse-5.8.1.txz Installing /packages/All/py37-numpy-1.16.6,1.txz Installing /packages/All/freetype2-2.10.2.txz ===== Message from freetype2-2.10.2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/png-1.6.37.txz Installing /packages/All/fontconfig-2.13.92_2,1.txz Running fc-cache to build fontconfig cache... Font directories: /usr/local/share/fonts /usr/local/lib/X11/fonts /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded Installing /packages/All/tcl86-8.6.10.txz Installing /packages/All/py37-six-1.15.0.txz Installing /packages/All/py37-cycler-0.10.0.txz Installing /packages/All/py37-dateutil-2.8.1.txz Installing /packages/All/py37-pytz-2020.1,1.txz Installing /packages/All/py37-pyparsing-2.4.7.txz Installing /packages/All/py37-tornado-5.1.1.txz Installing /packages/All/py37-kiwisolver-1.1.0,1.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.13.1.txz Installing /packages/All/libX11-1.6.12,1.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/tk86-8.6.10_1.txz Installing /packages/All/py37-tkinter-3.7.9_6.txz Installing /packages/All/py37-matplotlib-2.2.4_2.txz Installing /packages/All/py37-scipy-1.2.2_1.txz Installing /packages/All/hdf-szip-2.1.1.txz Installing /packages/All/hdf5-1.10.6,1.txz Installing /packages/All/lzo2-2.10_1.txz Installing /packages/All/ucl-1.03_5.txz ===== Message from ucl-1.03_5: -- ===> NOTICE: The ucl port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/py37-numexpr-2.7.1.txz Installing /packages/All/py37-mock-3.0.5.txz Installing /packages/All/py37-tables-3.5.2_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:01:11 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by GroopM-0.3.4_3 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by GroopM-0.3.4_3 for building => SHA256 Checksum OK for GroopM-0.3.4.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by GroopM-0.3.4_3 for building ===> Extracting for GroopM-0.3.4_3 => SHA256 Checksum OK for GroopM-0.3.4.tar.gz. Extracted Memory Use: 0.65M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for GroopM-0.3.4_3 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on package: py37-setuptools>0 - found ===> GroopM-0.3.4_3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on package: py37-setuptools>0 - found ===> GroopM-0.3.4_3 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for GroopM-0.3.4_3 running config SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for GroopM-0.3.4_3 running build running build_py creating build creating build/lib creating build/lib/groopm copying groopm/PCA.py -> build/lib/groopm copying groopm/rainbow.py -> build/lib/groopm copying groopm/profileManager.py -> build/lib/groopm copying groopm/ellipsoid.py -> build/lib/groopm copying groopm/som.py -> build/lib/groopm copying groopm/bin.py -> build/lib/groopm copying groopm/mstore.py -> build/lib/groopm copying groopm/__init__.py -> build/lib/groopm copying groopm/groopmExceptions.py -> build/lib/groopm copying groopm/groopm.py -> build/lib/groopm copying groopm/binManager.py -> build/lib/groopm copying groopm/torusMesh.py -> build/lib/groopm copying groopm/groopmTimekeeper.py -> build/lib/groopm copying groopm/groopmUtils.py -> build/lib/groopm copying groopm/cluster.py -> build/lib/groopm copying groopm/refine.py -> build/lib/groopm running build_scripts creating build/scripts-3.7 copying and adjusting bin/groopm -> build/scripts-3.7 changing mode of build/scripts-3.7/groopm from 644 to 755 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> GroopM-0.3.4_3 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> GroopM-0.3.4_3 depends on package: py37-matplotlib>=1.1.0 - found ===> GroopM-0.3.4_3 depends on package: py37-scipy>=0.10.1 - found ===> GroopM-0.3.4_3 depends on package: py37-tables>=2.3 - found ===> GroopM-0.3.4_3 depends on package: py37-setuptools>0 - found ===> GroopM-0.3.4_3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for GroopM-0.3.4_3 ===> GroopM-0.3.4_3 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> GroopM-0.3.4_3 depends on package: py37-matplotlib>=1.1.0 - found ===> GroopM-0.3.4_3 depends on package: py37-scipy>=0.10.1 - found ===> GroopM-0.3.4_3 depends on package: py37-tables>=2.3 - found ===> GroopM-0.3.4_3 depends on package: py37-setuptools>0 - found ===> GroopM-0.3.4_3 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list running install running build running build_py running build_scripts running install_lib creating /construction/biology/groopm/stage/usr/local/lib/python3.7 creating /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages creating /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/bin.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/profileManager.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/groopmExceptions.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/torusMesh.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/ellipsoid.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/groopmUtils.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/binManager.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/refine.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/groopmTimekeeper.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/__init__.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/cluster.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/PCA.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/som.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/rainbow.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/mstore.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm copying build/lib/groopm/groopm.py -> /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/bin.py to bin.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/bin.py", line 158 print " BIN:",deadBin.id,"will be consumed by BIN:",self.id ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(" BIN:",deadBin.id,"will be consumed by BIN:",self.id)? byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/profileManager.py to profileManager.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/profileManager.py", line 182 print "Loading data from:", self.dbFileName ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Loading data from:", self.dbFileName)? byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/groopmExceptions.py to groopmExceptions.cpython-37.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/torusMesh.py to torusMesh.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/torusMesh.py", line 253 print sys.exc_info()[0] ^ SyntaxError: invalid syntax byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/ellipsoid.py to ellipsoid.cpython-37.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/groopmUtils.py to groopmUtils.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/groopmUtils.py", line 129 print "Error when guessing contig file mimetype" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Error when guessing contig file mimetype")? byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/binManager.py to binManager.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/binManager.py", line 185 print "Number of stoits != 3. You need to transform" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Number of stoits != 3. You need to transform")? byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/refine.py to refine.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/refine.py", line 153 print " Start automatic bin refinement" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(" Start automatic bin refinement")? byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/groopmTimekeeper.py to groopmTimekeeper.cpython-37.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/cluster.py to cluster.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/cluster.py", line 169 print "****************************************************************" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("****************************************************************")? byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/PCA.py to PCA.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/PCA.py", line 82 print len(A), len(self.sumvariance), len(self.eigen) ^ SyntaxError: invalid syntax byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/som.py to som.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/som.py", line 231 print " Start SOM training. Side: %d Max: %d iterations" % (self.side, iterations) ^ SyntaxError: invalid syntax byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/rainbow.py to rainbow.cpython-37.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/mstore.py to mstore.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/mstore.py", line 82 print """ERROR: There was an error importing BamM. This probably means that BamM is not installed properly or not in your PYTHONPATH. Installation instructions for BamM are located at: http://minillinim.github.io/BamM If you're sure that BamM is installed (properly) then check your PYTHONPATH. If you still encounter this error. Please lodge a bug report at: http://githum.com/minillinim/BamM/issues Exiting... -------------------------------------------------------------------------------- """ ^ SyntaxError: invalid syntax byte-compiling /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/groopm/groopm.py to groopm.cpython-37.pyc File "/usr/local/lib/python3.7/site-packages/groopm/groopm.py", line 103 print "*******************************************************************************" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("*******************************************************************************")? writing byte-compilation script '/tmp/tmpq32ox753.py' /usr/local/bin/python3.7 /tmp/tmpq32ox753.py File "/usr/local/lib/python3.7/site-packages/groopm/bin.py", line 158 print " BIN:",deadBin.id,"will be consumed by BIN:",self.id ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(" BIN:",deadBin.id,"will be consumed by BIN:",self.id)? File "/usr/local/lib/python3.7/site-packages/groopm/profileManager.py", line 182 print "Loading data from:", self.dbFileName ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Loading data from:", self.dbFileName)? File "/usr/local/lib/python3.7/site-packages/groopm/torusMesh.py", line 253 print sys.exc_info()[0] ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.7/site-packages/groopm/groopmUtils.py", line 129 print "Error when guessing contig file mimetype" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Error when guessing contig file mimetype")? File "/usr/local/lib/python3.7/site-packages/groopm/binManager.py", line 185 print "Number of stoits != 3. You need to transform" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Number of stoits != 3. You need to transform")? File "/usr/local/lib/python3.7/site-packages/groopm/refine.py", line 153 print " Start automatic bin refinement" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(" Start automatic bin refinement")? File "/usr/local/lib/python3.7/site-packages/groopm/cluster.py", line 169 print "****************************************************************" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("****************************************************************")? File "/usr/local/lib/python3.7/site-packages/groopm/PCA.py", line 82 print len(A), len(self.sumvariance), len(self.eigen) ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.7/site-packages/groopm/som.py", line 231 print " Start SOM training. Side: %d Max: %d iterations" % (self.side, iterations) ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.7/site-packages/groopm/mstore.py", line 82 print """ERROR: There was an error importing BamM. This probably means that BamM is not installed properly or not in your PYTHONPATH. Installation instructions for BamM are located at: http://minillinim.github.io/BamM If you're sure that BamM is installed (properly) then check your PYTHONPATH. If you still encounter this error. Please lodge a bug report at: http://githum.com/minillinim/BamM/issues Exiting... -------------------------------------------------------------------------------- """ ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.7/site-packages/groopm/groopm.py", line 103 print "*******************************************************************************" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("*******************************************************************************")? removing /tmp/tmpq32ox753.py running install_egg_info running egg_info creating GroopM.egg-info writing GroopM.egg-info/PKG-INFO writing dependency_links to GroopM.egg-info/dependency_links.txt writing requirements to GroopM.egg-info/requires.txt writing top-level names to GroopM.egg-info/top_level.txt writing manifest file 'GroopM.egg-info/SOURCES.txt' reading manifest file 'GroopM.egg-info/SOURCES.txt' writing manifest file 'GroopM.egg-info/SOURCES.txt' Copying GroopM.egg-info to /construction/biology/groopm/stage/usr/local/lib/python3.7/site-packages/GroopM-0.3.4-py3.7.egg-info running install_scripts copying build/scripts-3.7/groopm -> /construction/biology/groopm/stage/usr/local/bin changing mode of /construction/biology/groopm/stage/usr/local/bin/groopm to 755 writing list of installed files to '/construction/biology/groopm/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for GroopM-0.3.4_3 file sizes/checksums [32]: 0% file sizes/checksums [32]: 100% packing files [32]: 0% packing files [32]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:01:23