I have these 3 commands that compile my program:
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"AESBest.d" -MT"AESBest.d" -o "AESBest.o" "AESBest.cpp"
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"main.d" -MT"main.d" -o "main.o" "main.cpp"
g++ -L/usr/include/cryptopp -o "Crypto" AESBest.o main.o -lcryptopp -lpthread
How is possible to create a makefile considering these 3 commands?
In Eclipse I receive output from the program in the shell, but in my bash, when I compile the bin file called "Crypto" and launch it, I have no output in my bash shell.
Why?
This will work:
all:
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"AESBest.d" -MT"AESBest.d" -o "AESBest.o" "AESBest.cpp"
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"main.d" -MT"main.d" -o "main.o" "main.cpp"
g++ -L/usr/include/cryptopp -o "Crypto" AESBest.o main.o -lcryptopp -lpthread
And you can break it down a little like this:
AESBest.o:
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"AESBest.d" -MT"AESBest.d" -o "AESBest.o" "AESBest.cpp"
main.o:
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"main.d" -MT"main.d" -o "main.o" "main.cpp"
Crypto:
g++ -L/usr/include/cryptopp -o "Crypto" AESBest.o main.o -lcryptopp -lpthread
And then simplify like this:
AESBest.o main.o: %.o : %.cpp
g++ -I/usr/include/cryptopp -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF$*.d -MT$*.d -o $# $<
Crypto: AESBest.o main.o
g++ -L/usr/include/cryptopp -o $# $^ -lcryptopp -lpthread
Related
I get an error saying
fatal error: stm32l0xx_hw_conf.h: No such file or directory
even though I have included stm32l0xx_hw_conf.h in the same project. How do I solve this error?
Edit: The console output for this error is:
Invoking: MCU GCC Compiler
/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Debug
arm-none-eabi-gcc -mcpu=cortex-m0plus -mthumb -mfloat-abi=soft
-DHAL_OK -DSTM32L0 -DSTM32L071xx -DUSE_MIROMICO_FMLR -DUSE_HAL_DRIVER -DUSE_BAND_868 -DSENSOR_ENABLED -DDEBUG -I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/inc"
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy"
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I/home/dinesh/fmlr_bitbucket/lorawan/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc"
-I../../../../../../../../Drivers/CMSIS/Device/ST/STM32L1xx/Include -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/CMSIS/Device/ST/STM32L0xx/Include"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/FMLR" -I../../../../../../../../Drivers/STM32L1xx_HAL_Driver/Inc -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/STM32L0xx_HAL_Driver/Inc"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/CMSIS/Include" -I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Crypto"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Mac"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Phy"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Utilities"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/Common" -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/sts_sht_21"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/bmp280" -I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Core"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/sx1272mb2das" -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/sx1272mb2das/Phy" -Og -g3 -Wall -fmessage-length=0 -ffunction-sections -c -fmessage-length=0 -MMD -MP -MF"Projects/MultiSensorHub/src/debug.d" -MT"Projects/MultiSensorHub/src/debug.o" -o "Projects/MultiSensorHub/src/debug.o"
"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/src/debug.c"
/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Debug
arm-none-eabi-gcc -mcpu=cortex-m0plus -mthumb -mfloat-abi=soft
-DHAL_OK -DSTM32L0 -DSTM32L071xx -DUSE_MIROMICO_FMLR -DUSE_HAL_DRIVER -DUSE_BAND_868 -DSENSOR_ENABLED -DDEBUG -I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/inc"
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy"
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I/home/dinesh/fmlr_bitbucket/lorawan/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc"
-I../../../../../../../../Drivers/CMSIS/Device/ST/STM32L1xx/Include -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/CMSIS/Device/ST/STM32L0xx/Include"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/FMLR" -I../../../../../../../../Drivers/STM32L1xx_HAL_Driver/Inc -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/STM32L0xx_HAL_Driver/Inc"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/CMSIS/Include" -I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Crypto"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Mac"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Phy"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Utilities"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/Common" -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/sts_sht_21"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/bmp280" -I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Core"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/sx1272mb2das" -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/sx1272mb2das/Phy" -Og -g3 -Wall -fmessage-length=0 -ffunction-sections -c -fmessage-length=0 -MMD -MP -MF"Projects/MultiSensorHub/src/hw_gpio.d" -MT"Projects/MultiSensorHub/src/hw_gpio.o" -o "Projects/MultiSensorHub/src/hw_gpio.o"
"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/src/hw_gpio.c"
/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Debug
arm-none-eabi-gcc -mcpu=cortex-m0plus -mthumb -mfloat-abi=soft
-DHAL_OK -DSTM32L0 -DSTM32L071xx -DUSE_MIROMICO_FMLR -DUSE_HAL_DRIVER -DUSE_BAND_868 -DSENSOR_ENABLED -DDEBUG -I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/inc"
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy"
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc
-I/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I/home/dinesh/fmlr_bitbucket/lorawan/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc/Legacy"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/SW4STM32/Miromico-FMLR/Drivers/STM32L0xx_HAL_Driver/Inc"
-I../../../../../../../../Drivers/CMSIS/Device/ST/STM32L1xx/Include -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/CMSIS/Device/ST/STM32L0xx/Include"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/FMLR" -I../../../../../../../../Drivers/STM32L1xx_HAL_Driver/Inc -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/STM32L0xx_HAL_Driver/Inc"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/CMSIS/Include" -I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Crypto"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Mac"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Phy"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Utilities"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/Common" -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/sts_sht_21"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/Components/bmp280" -I"/home/dinesh/fmlr_bitbucket/lorawan/Middlewares/Third_Party/Lora/Core"
-I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/sx1272mb2das" -I"/home/dinesh/fmlr_bitbucket/lorawan/Drivers/BSP/sx1272mb2das/Phy" -Og -g3 -Wall -fmessage-length=0 -ffunction-sections -c -fmessage-length=0 -MMD -MP -MF"Projects/MultiSensorHub/src/bsp.d" -MT"Projects/MultiSensorHub/src/bsp.o" -o "Projects/MultiSensorHub/src/bsp.o"
"/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/src/bsp.c"
In file included from
/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/inc/hw.h:72:0,from
/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/src/bsp.c:50:
/home/dinesh/fmlr_bitbucket/lorawan/Projects/Multi/Applications/LoRa/MultiSensorHub/inc/hw_conf.h:123:10:
fatal error: stm32l0xx_hw_conf.h: No such file or directory #include
"stm32l0xx_hw_conf.h"
You need to set the path to the include file in the project setting (if its a managed project) or the makefile if it is not. Adding a file to the project does not add it to the include path.
It is possible you need to re-index the project. In Eclipse, you can right click the project and select Index->Rebuild.
Runing the command in the instruction:
pip install -U spacy
It fails to build wheel for Building wheels for collected packages: spacy, murmurhash, cymem, preshed, thinc, ujson, regex, cytoolz
This is the error shown on the terminal.
Running setup.py bdist_wheel for spacy ... error
Complete output from command /usr/local/opt/python/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-install-9ygkdvbw/spacy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-wheel-swjw2gll --python-tag cp36:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.6
creating build/lib.macosx-10.13-x86_64-3.6/spacy
copying spacy/lemmatizer.py -> build/lib.macosx-10.13-x86_64-3.6/spacy
copying spacy/compat.py -> build/lib.macosx-10.13-x86_64-3.6/spacy
...
...
copying spacy/tests/tokenizer/sun.txt -> build/lib.macosx-10.13-x86_64-3.6/spacy/tests/tokenizer
running build_ext
building 'spacy.parts_of_speech' extension
creating build/temp.macosx-10.13-x86_64-3.6
creating build/temp.macosx-10.13-x86_64-3.6/spacy
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes /usr/local/opt/openssl/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-install-9ygkdvbw/spacy/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c spacy/parts_of_speech.cpp -o build/temp.macosx-10.13-x86_64-3.6/spacy/parts_of_speech.o -O2 -Wno-strict-prototypes -Wno-unused-function
clang: warning: /usr/local/opt/openssl/include: 'linker' input unused [-Wunused-command-line-argument]
clang++ -bundle -undefined dynamic_lookup /usr/local/opt/openssl/lib /usr/local/opt/openssl/include build/temp.macosx-10.13-x86_64-3.6/spacy/parts_of_speech.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.13-x86_64-3.6/spacy/parts_of_speech.cpython-36m-darwin.so -Wl,-rpath,#loader_path/../spacy/platform/darwin/lib
ld: can't map file, errno=22 file '/usr/local/opt/openssl/include' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'clang++' failed with exit status 1
----------------------------------------
Failed building wheel for spacy
Running setup.py clean for spacy
Running setup.py bdist_wheel for murmurhash ... error
Complete output from command /usr/local/opt/python/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-install-9ygkdvbw/murmurhash/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-wheel-9ytvwkua --python-tag cp36:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.6
creating build/lib.macosx-10.13-x86_64-3.6/murmurhash
copying murmurhash/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/murmurhash
copying murmurhash/about.py -> build/lib.macosx-10.13-x86_64-3.6/murmurhash
creating build/lib.macosx-10.13-x86_64-3.6/murmurhash/tests
copying murmurhash/tests/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/murmurhash/tests
copying murmurhash/tests/test_import.py -> build/lib.macosx-10.13-x86_64-3.6/murmurhash/tests
copying murmurhash/mrmr.pyx -> build/lib.macosx-10.13-x86_64-3.6/murmurhash
copying murmurhash/__init__.pxd -> build/lib.macosx-10.13-x86_64-3.6/murmurhash
copying murmurhash/mrmr.pxd -> build/lib.macosx-10.13-x86_64-3.6/murmurhash
creating build/lib.macosx-10.13-x86_64-3.6/murmurhash/include
creating build/lib.macosx-10.13-x86_64-3.6/murmurhash/include/murmurhash
copying murmurhash/include/murmurhash/MurmurHash2.h -> build/lib.macosx-10.13-x86_64-3.6/murmurhash/include/murmurhash
copying murmurhash/include/murmurhash/MurmurHash3.h -> build/lib.macosx-10.13-x86_64-3.6/murmurhash/include/murmurhash
running build_ext
building 'murmurhash.mrmr' extension
creating build/temp.macosx-10.13-x86_64-3.6
creating build/temp.macosx-10.13-x86_64-3.6/murmurhash
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes /usr/local/opt/openssl/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-install-9ygkdvbw/murmurhash/murmurhash/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c murmurhash/mrmr.cpp -o build/temp.macosx-10.13-x86_64-3.6/murmurhash/mrmr.o -O3 -Wno-strict-prototypes -Wno-unused-function
clang: warning: /usr/local/opt/openssl/include: 'linker' input unused [-Wunused-command-line-argument]
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes /usr/local/opt/openssl/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-install-9ygkdvbw/murmurhash/murmurhash/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c murmurhash/MurmurHash2.cpp -o build/temp.macosx-10.13-x86_64-3.6/murmurhash/MurmurHash2.o -O3 -Wno-strict-prototypes -Wno-unused-function
clang: warning: /usr/local/opt/openssl/include: 'linker' input unused [-Wunused-command-line-argument]
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes /usr/local/opt/openssl/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/private/var/folders/9t/0qgpwgy906z_sww71dnkgkr80000gn/T/pip-install-9ygkdvbw/murmurhash/murmurhash/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c murmurhash/MurmurHash3.cpp -o build/temp.macosx-10.13-x86_64-3.6/murmurhash/MurmurHash3.o -O3 -Wno-strict-prototypes -Wno-unused-function
clang: warning: /usr/local/opt/openssl/include: 'linker' input unused [-Wunused-command-line-argument]
clang++ -bundle -undefined dynamic_lookup /usr/local/opt/openssl/lib /usr/local/opt/openssl/include build/temp.macosx-10.13-x86_64-3.6/murmurhash/mrmr.o build/temp.macosx-10.13-x86_64-3.6/murmurhash/MurmurHash2.o build/temp.macosx-10.13-x86_64-3.6/murmurhash/MurmurHash3.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.13-x86_64-3.6/murmurhash/mrmr.cpython-36m-darwin.so
ld: can't map file, errno=22 file '/usr/local/opt/openssl/lib' for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'clang++' failed with exit status 1
----------------------------------------
Failed building wheel for murmurhash
Running setup.py clean for murmurhash
Similar error for the rest of the libraries.
It probably has something to do with finding python header files. And I checked the location using this command :
python -c "import sysconfig; print(sysconfig.get_config_var('INCLUDEPY'))"
/usr/local/opt/python/Frameworks/Python.framework/Versions/3.6/include/python3.6m
It has all the header files.
This answer (Failed building wheel for spacy) suggests installing the wheel individually. How do I do that on Mac OS X?
The best way to download Spacy and work with it is to download it manually and link it. Below command is used to download it and link it to your python libraries:
Command to download it:
pip install https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.2.0/en_core_web_sm-2.2.0.tar.gz
Link that will explain more: https://spacy.io/usage/models#usage-link
I’m using the Random Forest library for Matlab (link). I’m using it for classification. On Windows it works very well out of the box (precombiled mex files) but I also want to run it on a CentOS cluster.
I have tried to compile it on the cluster by executing make mex but I’m getting an error. The output is as follows:
rm twonorm_test -rf
rm tempbuild/*.o *.o -rf
rm *~ -rf
rm *.mexw32 twonorm_test -rf
rm *.mexa64 -rf
rm classRF -rf
rm *.exe -rf
echo 'Compiling classTree.cpp'
Compiling classTree.cpp
g++ -fpic -O2 -funroll-loops -msse3 -c src/classTree.cpp -o tempbuild/classTree.o
echo 'Compiling Cokus (random number generator)'
Compiling Cokus (random number generator)
g++ -fpic -O2 -funroll-loops -msse3 -c src/cokus.cpp -o tempbuild/cokus.o
echo 'Compiling rfsub.f (fortran subroutines)'
Compiling rfsub.f (fortran subroutines)
gfortran -O2 -fpic -c src/rfsub.f -o rfsub.o
echo 'Compiling rfutils.cpp'
Compiling rfutils.cpp
g++ -fpic -O2 -funroll-loops -msse3 -c src/rfutils.cpp -o tempbuild/rfutils.o
echo 'Generating Mex'
Generating Mex
mex src/mex_ClassificationRF_train.cpp src/classRF.cpp tempbuild/classTree.o tempbuild/rfutils.o rfsub.o tempbuild/cokus.o -o mexClassRF_train -lgfortran -lm -DMATLAB -g
Unknown MEX argument '-o'.
make: *** [mex_classRF] Error 255
Does somebody knows how to solve this issue? If you want, you can take RF_MexStandalone-v0.02.zip from the above link and then go to randomforest-matlab/RF_Reg_C/Makefile.
Edit: I have change -o to -output but now the output is the following:
rm twonorm_test -rf
rm tempbuild/*.o *.o -rf
rm *~ -rf
rm *.mexw32 twonorm_test -rf
rm *.mexa64 -rf
rm classRF -rf
rm *.exe -rf
echo 'Compiling classTree.cpp'
Compiling classTree.cpp
g++ -fpic -O2 -funroll-loops -msse3 -c src/classTree.cpp -o tempbuild/classTree.o
echo 'Compiling Cokus (random number generator)'
Compiling Cokus (random number generator)
g++ -fpic -O2 -funroll-loops -msse3 -c src/cokus.cpp -o tempbuild/cokus.o
echo 'Compiling rfsub.f (fortran subroutines)'
Compiling rfsub.f (fortran subroutines)
gfortran -O2 -fpic -c src/rfsub.f -o rfsub.o
echo 'Compiling rfutils.cpp'
Compiling rfutils.cpp
g++ -fpic -O2 -funroll-loops -msse3 -c src/rfutils.cpp -o tempbuild/rfutils.o
echo 'Generating Mex'
Generating Mex
mex src/mex_ClassificationRF_train.cpp src/classRF.cpp tempbuild/classTree.o tempbuild/rfutils.o rfsub.o tempbuild/cokus.o -output mexClassRF_train -lgfortran -lm -DMATLAB -g
Building with 'g++'.
cc1plus: error: unrecognized command line option "-std=c++11"
make: *** [mex_classRF] Error 255
I did not find an option -std=c++11 in the makefile.
The error is quite self-explanatory: the option -o is not recognized. If you type mex -help you see the options mex accepts. Try to replace -o with -output.
EDIT regarding the std=c++11 option, you are probably using an old version of gcc compiler. You can either change it to std=c++0x which is the equivalent option (but note that some features of the c++11 standard may not be present\implemented), or upgrade to an up-to-date version of gcc.
If you need more help, please report the output of g++ --version.
I am having trouble with ImageMagik on CentOS.
The error is:
Error: identify: no decode delegate for this image format `PNG' #
error/constitute.c/ReadImage/501.
convert -list configure
Path: /usr/lib64/ImageMagick-6.5.4/config/configure.xml
Name Value
-------------------------------------------------------------------------------
CC gcc -std=gnu99
CFLAGS -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -W -pthread
CONFIGURE ./configure '--build=x86_64-redhat-linux-gnu' '--host=x86_64-redhat-linux-gnu' '--target=x86_64-redhat-linux-gnu' '--program-prefix=' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin' '--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share' '--includedir=/usr/include' '--libdir=/usr/lib64' '--libexecdir=/usr/libexec' '--localstatedir=/var' '--sharedstatedir=/var/lib' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--enable-shared' '--disable-static' '--with-modules' '--with-perl' '--with-x' '--with-threads' '--with-magick_plus_plus' '--with-gslib' '--with-wmf' '--with-lcms' '--with-rsvg' '--with-xml' '--with-perl-options=INSTALLDIRS=vendor CC='\''gcc -L/builddir/build/BUILD/ImageMagick-6.5.4-7/magick/.libs'\'' LDDLFLAGS='\''-shared -L/builddir/build/BUILD/ImageMagick-6.5.4-7/magick/.libs'\''' '--without-dps' '--without-included-ltdl' '--with-ltdl-include=/usr/include' '--with-ltdl-lib=/usr/lib64' 'build_alias=x86_64-redhat-linux-gnu' 'host_alias=x86_64-redhat-linux-gnu' 'target_alias=x86_64-redhat-linux-gnu' 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' 'CXXFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
COPYRIGHT Copyright (C) 1999-2009 ImageMagick Studio LLC
CPPFLAGS -I/usr/include/ImageMagick
CXX g++
CXXFLAGS -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -W -pthread
DEFS -DHAVE_CONFIG_H
DELEGATES bzlib fontconfig freetype gs jpeg jng jp2 lcms openexr png rsvg tiff x11 xml wmf zlib
DISTCHECK_CONFIG_FLAGS 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' --disable-deprecated --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with-dps=no --with-fontpath=
EXEC-PREFIX /usr
HOST x86_64-redhat-linux-gnu
LDFLAGS -L/usr/lib64 -lfreetype
LIB_VERSION 0x654
LIB_VERSION_NUMBER 6,5,4,7
LIBS -lMagickCore -llcms -ltiff -lfreetype -ljpeg -lfontconfig -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lgomp -lpthread -lltdl
NAME ImageMagick
PCFLAGS -fopenmp
PREFIX /usr
QuantumDepth 16
RELEASE_DATE 2014-02-10
VERSION 6.5.4
WEBSITE http://www.imagemagick.org
I can see "PNG" in the list of DELEGATES but there doesn't seem to be anything in the LIBS section (see above).
I have tried installing libpng, which is already installed and I've have re-installed ImageMagik from source but it still isn't working.
Any ideas?
configure attempts to configure with every available image delegate, so when you're building from source, you'll need to have the libpng-devel package installed. If for some reason it didn't detect it, you may want to try forcing it with --with-png=yes in your options to configure to get some feedback.
See http://www.imagemagick.org/script/advanced-unix-installation.php
I want to run R (the statistical package) from Perl in RedHat Linux. I found online that there is a package called RSPerl that does this job but I have hard time installing it in RedHat. This software requires R to be installed as a shared library. I followed the instructions but I am facing the following problem when (after installing R without problem) I try to install RSPerl.
[root#xxx opt]# R CMD INSTALL -c -l ./ RSPerl_0.92-1.tar.gz
* installing *source* package âRSPerlâ ...
checking for perl... /usr/bin/perl
No support for any of the Perl modules from calling Perl from R.
*****************************************************
Set PERL5LIB to /opt/RSPerl/perl
*****************************************************
Testing: -L/usr/local/lib64/R/lib -lR
Using '/usr/bin/perl' as the perl executable
Perl modules (no):
Adding R package to list of Perl modules to enable callbacks to R from Perl
Creating the C code for dynamically loading modules with native code for Perl: R
modules: R; linking:
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Support R in Perl: yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating inst/scripts/RSPerl.csh
config.status: creating inst/scripts/RSPerl.bsh
config.status: creating src/RinPerlMakefile
config.status: creating src/Makefile.PL
config.status: creating cleanup
config.status: creating src/R.pm
config.status: creating R/perl5lib.R
making target all in RinPerlMakefile
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c Converters.c -o Converters.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c Reflectance.c -o Reflectance.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c ForeignReference.c -o ForeignReference.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c UserConverters.c -o UserConverters.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c GeneralConverters.c -o GeneralConverters.o
making libPerlConverter.so
/usr/local/lib64/R/bin/R CMD SHLIB -o libPerlConverter.so Converters.c Reflectance.c ForeignReference.c UserConverters.o GeneralConverters.o
make[1]: Entering directory `/tmp/RtmpSqebDp/R.INSTALL68be5031/RSPerl/src'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o libPerlConverter.so Converters.o Reflectance.o ForeignReference.o UserConverters.o GeneralConverters.o -Wl,-E -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/DynaLoader/DynaLoader.a -L/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -lperl -lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc -L/usr/local/lib64/R/lib -lR
make[1]: Leaving directory `/tmp/RtmpSqebDp/R.INSTALL68be5031/RSPerl/src'
if test ! -d /opt/RSPerl/libs ; then mkdir /opt/RSPerl/libs ; fi
cp libPerlConverter.so /opt/RSPerl/libs
Makefile.PL PREFIX=/opt/RSPerl LIB=/opt/RSPerl/perl
make: Makefile.PL: Command not found
make: *** [Makefile.perl] Error 127
calling make -f Makefile.perl install
make: Makefile.perl: No such file or directory
make: *** No rule to make target `Makefile.perl'. Stop.
chmod: cannot access `blib/lib/R.pm': No such file or directory
Finished configuration
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c RPerlElements.c -o RPerlElements.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c RPerlEval.c -o RPerlEval.o
RPerlEval.c: In function âRS_PerlEvalStringâ:
RPerlEval.c:20: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function âRS_PerlGetâ:
RPerlEval.c:128: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function âRS_PerlCallModifiedâ:
RPerlEval.c:208: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function âRS_PerlCallâ:
RPerlEval.c:377: warning: ISO C90 forbids mixed declarations and code
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c RPerlInit.c -o RPerlInit.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c RPerlNew.c -o RPerlNew.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c RPerlReference.c -o RPerlReference.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c RPerlVars.c -o RPerlVars.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c Utils.c -o Utils.o
Utils.c: In function âcharacterVectorToNullTerminatedArrayâ:
Utils.c:35: warning: assignment discards qualifiers from pointer target type
Utils.c: In function âcharacterVectorToArrayâ:
Utils.c:78: warning: assignment discards qualifiers from pointer target type
gcc -std=gnu99 -I/usr/local/lib64/R/include -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fpic -g -O2 -c xsinit.c -o xsinit.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o RSPerl.so Converters.o ForeignReference.o GeneralConverters.o RPerlElements.o RPerlEval.o RPerlInit.o RPerlNew.o RPerlReference.o RPerlVars.o Reflectance.o UserConverters.o Utils.o xsinit.o -Wl,-E -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/DynaLoader/DynaLoader.a -L/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -lperl -lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc -L/usr/local/lib64/R/lib -lR
installing to /opt/RSPerl/libs
** R
** inst
** preparing package for lazy loading
** help
Warning: /tmp/RtmpSqebDp/R.INSTALL68be5031/RSPerl/man/PerlReferenceObjects.Rd:32: unknown macro '\textit'
*** installing help indices
** building package indices ...
Removing additional files
rm: cannot remove `src/Makefile.perl': No such file or directory
rm: cannot remove `src/pm_to_blib': No such file or directory
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/RSPerl/libs/RSPerl.so':
/opt/RSPerl/libs/RSPerl.so: undefined symbol: boot_R
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/opt/RSPerlâ
* restoring previous â/opt/RSPerlâ
[root#xxx opt]#
My system information is the following:
Linux version 2.6.18-194.el5 (mockbuild#x86-005.build.bos.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)) #1 SMP Tue Mar 16 21:52:39 EDT 2010
and it runs on a 64 bit Xeon server.
Do you have any idea what's going on?
Thank you in advance.
From R-2.12 they remove requirement on perl, hence the PERL (env variable) in lib/R/etc/Renviron will not be set anymore.
One quick fix is to manually set PERL, as following:
PERL=`which perl` R --vanilla CMD INSTALL -c -l ~/library/ RSPerl_0.92-1.tar.gz
make sure you get perl-dev, not only perl (e.g. under ubuntu, apt-get install libperl-dev, if you compiled perl yourself, this won't be a problem)
RSPerl is an interface between R (or S) and Perl. It looks like you need to do some more research and find a Perl package that fits your installation or if you do have a compatible version use a compiler flag or an environment variable that tells R where to find it. Then install RSPerl.
You might want to look at this example of setting environment variables from an admittedly old posting from Duncan Temple Lang.