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olgabot/installation_log.txt

Created June 23, 2017 17:46
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Installing ExpressionMatrix
Raw
installation_log.txt
(maca) ➜ ExpressionMatrix2 git:(master) conda create -n ExpressionMatrix2 python=3 boost graphviz
Fetching package metadata ...............
Solving package specifications: .
Package plan for installation in environment /Users/olgabot/anaconda3/envs/ExpressionMatrix2:
The following NEW packages will be INSTALLED:
boost: 1.61.0-py36_0
freetype: 2.5.5-2
graphviz: 2.38.0-4
icu: 54.1-0
jbig: 2.1-0
jpeg: 9b-0
libpng: 1.6.27-0
libtiff: 4.0.6-3
openssl: 1.0.2l-0
pip: 9.0.1-py36_1
python: 3.6.1-2
readline: 6.2-2
setuptools: 27.2.0-py36_0
sqlite: 3.13.0-0
tk: 8.5.18-0
wheel: 0.29.0-py36_0
xz: 5.2.2-1
zlib: 1.2.8-3
Proceed ([y]/n)? y
jpeg-9b-0.tar. 100% |###############################################################################################################| Time: 0:00:00 3.93 MB/s
boost-1.61.0-p 100% |###############################################################################################################| Time: 0:00:01 14.09 MB/s
graphviz-2.38. 100% |###############################################################################################################| Time: 0:00:00 16.50 MB/s
#
# To activate this environment, use:
# > source activate ExpressionMatrix2
#
# To deactivate this environment, use:
# > source deactivate ExpressionMatrix2
#
(maca) ➜ ExpressionMatrix2 git:(master) source activate ExpressionMatrix2
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) ls
Debug LICENSE README.md Release bin doc src tests
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) ll
total 16
drwxr-xr-x 6 olgabot staff 204B Jun 23 10:30 Debug
-rw-r--r-- 1 olgabot staff 1.1K Jun 23 10:30 LICENSE
-rw-r--r-- 1 olgabot staff 3.6K Jun 23 10:30 README.md
drwxr-xr-x 6 olgabot staff 204B Jun 23 10:30 Release
drwxr-xr-x 3 olgabot staff 102B Jun 23 10:30 bin
drwxr-xr-x 12 olgabot staff 408B Jun 23 10:30 doc
drwxr-xr-x 59 olgabot staff 2.0K Jun 23 10:30 src
drwxr-xr-x 3 olgabot staff 102B Jun 23 10:30 tests
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) ls tests
ToyTest1
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) ll tests
total 0
drwxr-xr-x 6 olgabot staff 204B Jun 23 10:30 ToyTest1
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) cp tests tests_copy
cp: tests is a directory (not copied).
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) cp -r tests tests_copy
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) ls bin
ubuntu-16.04
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) ls bin/ubuntu-16.04
2017-06-12
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) cd tests_copy/ToyTest1
(ExpressionMatrix2) ➜ ToyTest1 git:(master) cp ../../bin/ubuntu-16.04/2017-06-12/ExpressionMatrix2.so .
(ExpressionMatrix2) ➜ ToyTest1 git:(master) ls
ExpressionMatrix.csv ExpressionMatrix2.so MetaData.csv run.py runServer.py
(ExpressionMatrix2) ➜ ToyTest1 git:(master) python run.py
Traceback (most recent call last):
File "run.py", line 5, in <module>
import ExpressionMatrix2
ImportError: dlopen(/Users/olgabot/code/ExpressionMatrix2/tests_copy/ToyTest1/ExpressionMatrix2.so, 2): no suitable image found. Did find:
/Users/olgabot/code/ExpressionMatrix2/tests_copy/ToyTest1/ExpressionMatrix2.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03
/Users/olgabot/code/ExpressionMatrix2/tests_copy/ToyTest1/ExpressionMatrix2.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03
(ExpressionMatrix2) ➜ ToyTest1 git:(master) cd ..
(ExpressionMatrix2) ➜ tests_copy git:(master) cd ..
(ExpressionMatrix2) ➜ ExpressionMatrix2 git:(master) cd src
(ExpressionMatrix2) ➜ src git:(master) ls
BitSet.hpp MemoryMappedStringTable.hpp fstream.hpp
CZI_ASSERT.hpp MemoryMappedVector.hpp iosfwd.hpp
Cell.hpp MemoryMappedVectorOfLists.hpp iostream.hpp
CellSets.cpp MemoryMappedVectorOfVectors.hpp iterator.hpp
CellSets.hpp MurmurHash2.cpp map.hpp
CellSimilarityGraph.cpp MurmurHash2.hpp nextPowerOfTwo.hpp
CellSimilarityGraph.hpp PythonModule.cpp orderPairs.hpp
ExpressionMatrix.cpp PythonPair.hpp randIndex.hpp
ExpressionMatrix.hpp SimilarPairs.cpp set.hpp
ExpressionMatrixFindSimilarPairs.cpp SimilarPairs.hpp sstream.hpp
ExpressionMatrixHttpServer.cpp algorithm.hpp stdexcept.hpp
ExpressionMatrixLsh.cpp boost_array.hpp string.hpp
HttpServer.cpp boost_lexical_cast.hpp timestamp.hpp
HttpServer.hpp boost_tuple_tuple.hpp tokenize.cpp
Ids.hpp color.cpp tokenize.hpp
MemoryAsContainer.hpp color.hpp touchMemory.cpp
MemoryMappedObject.hpp cstddef.hpp touchMemory.hpp
MemoryMappedOpenAddressingHashTable.hpp cstdint.hpp utility.hpp
MemoryMappedStringTable.cpp deduplicate.hpp vector.hpp
(ExpressionMatrix2) ➜ src git:(master) cd ../Release
(ExpressionMatrix2) ➜ Release git:(master) ls
makefile objects.mk sources.mk src
(ExpressionMatrix2) ➜ Release git:(master) make all
Building file: ../src/CellSets.cpp
Invoking: GCC C++ Compiler
g++ -std=c++0x -I/usr/include/python3.5m -O3 -msse4.2 -Wall -Wconversion -c -fmessage-length=0 -fPIC -MMD -MP -MF"src/CellSets.d" -MT"src/CellSets.d" -o "src/CellSets.o" "../src/CellSets.cpp"
In file included from ../src/CellSets.cpp:1:
In file included from ../src/CellSets.hpp:5:
In file included from ../src/MemoryMappedVector.hpp:7:
../src/CZI_ASSERT.hpp:8:10: fatal error: 'boost/lexical_cast.hpp' file not found
#include <boost/lexical_cast.hpp>
^
1 error generated.
make: *** [src/CellSets.o] Error 1
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