sawsimeon
commented
8 years ago Same here, got an error when installing camb on Mac. here is the output
> library(devtools); install_github("cambDI/camb/camb"
+ )
Downloading GitHub repo cambDI/camb@master
from URL https://api.github.com/repos/cambDI/camb/zipball/master
Installing camb
Installing 1 package: quantreg
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 1881k 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0100 1881k 100 1881k 0 0 821k 0 0:00:02 0:00:02 --:--:-- 822k
tar: Failed to set default locale
The downloaded binary packages are in
/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T//RtmpQki79C/downloaded_packages
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \
--no-environ --no-save --no-restore --quiet CMD INSTALL \
'/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb' \
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library' \
--install-tests
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
* installing *source* package 'camb' ...
./configure: line 4: cmake: command not found
make: *** No targets specified and no makefile found. Stop.
** libs
** arch -
rm -f *.o
rm -f *.so
PKG_CXXFLAGS="-I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi" R CMD SHLIB -o camb.so GetProperties.cpp fingerprint.cpp standardise.cpp misc.cpp smindigo.cpp -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.6/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.7/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.8/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.9/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.10/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Linux/x64/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Linux/x86/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Win/x64/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Win/x86/lib -lindigo-static -lcommon -lmolecule -lreaction -llayout -lz -ltinyxml -lgraph -lindigo-inchi-static -lindigo-renderer-static -lpng -lpixman -lcairo -linchi -lrender2d -lindigo-static -lcommon -lmolecule -lreaction -llayout -lz -ltinyxml -lgraph -lindigo-inchi-static -lindigo-renderer-static -lpng -lpixman -lcairo -linchi -lrender2d -lindigo-static -lcommon -lmolecule -lreaction -llayout -lz -ltinyxml -lgraph -lindigo-inchi-static -lindigo-renderer-static -lpng -lpixman -lcairo -linchi -lrender2d
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -fPIC -Wall -mtune=core2 -g -O2 -c GetProperties.cpp -o GetProperties.o
GetProperties.cpp:83:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (structure = indigoNext(structureIter)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
GetProperties.cpp:83:26: note: place parentheses around the assignment to silence this warning
while (structure = indigoNext(structureIter)) {
^
( )
GetProperties.cpp:83:26: note: use '==' to turn this assignment into an equality comparison
while (structure = indigoNext(structureIter)) {
^
==
GetProperties.cpp:95:42: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (propFirst = indigoNext(propsFirst)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
GetProperties.cpp:95:42: note: place parentheses around the assignment to silence this warning
while (propFirst = indigoNext(propsFirst)) {
^
( )
GetProperties.cpp:95:42: note: use '==' to turn this assignment into an equality comparison
while (propFirst = indigoNext(propsFirst)) {
^
==
GetProperties.cpp:113:33: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (prop = indigoNext(props)) {
~~~~~^~~~~~~~~~~~~~~~~~~
GetProperties.cpp:113:33: note: place parentheses around the assignment to silence this warning
while (prop = indigoNext(props)) {
^
( )
GetProperties.cpp:113:33: note: use '==' to turn this assignment into an equality comparison
while (prop = indigoNext(props)) {
^
==
GetProperties.cpp:88:24: warning: unused variable 'target_value' [-Wunused-variable]
double target_value = 0;
^
GetProperties.cpp:54:14: warning: unused variable 'debug' [-Wunused-variable]
bool debug = false;
^
GetProperties.cpp:80:13: warning: unused variable 'propss' [-Wunused-variable]
int propss = 0;
^
GetProperties.cpp:184:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (structure = indigoNext(structureIter)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
GetProperties.cpp:184:26: note: place parentheses around the assignment to silence this warning
while (structure = indigoNext(structureIter)) {
^
( )
GetProperties.cpp:184:26: note: use '==' to turn this assignment into an equality comparison
while (structure = indigoNext(structureIter)) {
^
==
GetProperties.cpp:189:24: warning: unused variable 'target_value' [-Wunused-variable]
double target_value = 0;
^
GetProperties.cpp:160:14: warning: unused variable 'debug' [-Wunused-variable]
bool debug = false;
^
GetProperties.cpp:265:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (structure = indigoNext(structureIter)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
GetProperties.cpp:265:26: note: place parentheses around the assignment to silence this warning
while (structure = indigoNext(structureIter)) {
^
( )
GetProperties.cpp:265:26: note: use '==' to turn this assignment into an equality comparison
while (structure = indigoNext(structureIter)) {
^
==
GetProperties.cpp:271:38: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (propFirst = indigoNext(propsFirst)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
GetProperties.cpp:271:38: note: place parentheses around the assignment to silence this warning
while (propFirst = indigoNext(propsFirst)) {
^
( )
GetProperties.cpp:271:38: note: use '==' to turn this assignment into an equality comparison
while (propFirst = indigoNext(propsFirst)) {
^
==
GetProperties.cpp:267:24: warning: unused variable 'target_value' [-Wunused-variable]
double target_value = 0;
^
GetProperties.cpp:246:14: warning: unused variable 'debug' [-Wunused-variable]
bool debug = false;
^
13 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -fPIC -Wall -mtune=core2 -g -O2 -c fingerprint.cpp -o fingerprint.o
fingerprint.cpp:32:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(neighbour = indigoNext(neighbourIterator)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fingerprint.cpp:32:21: note: place parentheses around the assignment to silence this warning
while(neighbour = indigoNext(neighbourIterator)) {
^
( )
fingerprint.cpp:32:21: note: use '==' to turn this assignment into an equality comparison
while(neighbour = indigoNext(neighbourIterator)) {
^
==
fingerprint.cpp:48:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(neighbour = indigoNext(neighbourIterator)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fingerprint.cpp:48:21: note: place parentheses around the assignment to silence this warning
while(neighbour = indigoNext(neighbourIterator)) {
^
( )
fingerprint.cpp:48:21: note: use '==' to turn this assignment into an equality comparison
while(neighbour = indigoNext(neighbourIterator)) {
^
==
fingerprint.cpp:80:24: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(atom = indigoNext(atomIter)) {
~~~~~^~~~~~~~~~~~~~~~~~~~~~
fingerprint.cpp:80:24: note: place parentheses around the assignment to silence this warning
while(atom = indigoNext(atomIter)) {
^
( )
fingerprint.cpp:80:24: note: use '==' to turn this assignment into an equality comparison
while(atom = indigoNext(atomIter)) {
^
==
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -fPIC -Wall -mtune=core2 -g -O2 -c standardise.cpp -o standardise.o
standardise.cpp:133:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (structure = indigoNext(structureIter)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
standardise.cpp:133:26: note: place parentheses around the assignment to silence this warning
while (structure = indigoNext(structureIter)) {
^
( )
standardise.cpp:133:26: note: use '==' to turn this assignment into an equality comparison
while (structure = indigoNext(structureIter)) {
^
==
standardise.cpp:287:31: warning: incrementing expression of type bool is deprecated [-Wdeprecated-increment-bool]
highIodine++;
~~~~~~~~~~^
standardise.cpp:338:28: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (prop = indigoNext(props)) {
~~~~~^~~~~~~~~~~~~~~~~~~
standardise.cpp:338:28: note: place parentheses around the assignment to silence this warning
while (prop = indigoNext(props)) {
^
( )
standardise.cpp:338:28: note: use '==' to turn this assignment into an equality comparison
while (prop = indigoNext(props)) {
^
==
standardise.cpp:143:24: warning: unused variable 'target_value' [-Wunused-variable]
double target_value = 0;
^
standardise.cpp:127:24: warning: unused variable 'propFirst' [-Wunused-variable]
int props,prop,propFirst,propsFirst;
^
standardise.cpp:127:34: warning: unused variable 'propsFirst' [-Wunused-variable]
int props,prop,propFirst,propsFirst;
^
standardise.cpp:128:13: warning: unused variable 'propss' [-Wunused-variable]
int propss = 0;
^
standardise.cpp:129:13: warning: unused variable 'namesprop' [-Wunused-variable]
int namesprop = TRUE;
^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -fPIC -Wall -mtune=core2 -g -O2 -c misc.cpp -o misc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -fPIC -Wall -mtune=core2 -g -O2 -c smindigo.cpp -o smindigo.o
smindigo.cpp:34:9: warning: unused variable 'number' [-Wunused-variable]
int number = -1;
^
smindigo.cpp:71:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (match = indigoNext(matchIter)) {
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:71:22: note: place parentheses around the assignment to silence this warning
while (match = indigoNext(matchIter)) {
^
( )
smindigo.cpp:71:22: note: use '==' to turn this assignment into an equality comparison
while (match = indigoNext(matchIter)) {
^
==
smindigo.cpp:73:30: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (queryAtom = indigoNext(queryAtomIter))
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:73:30: note: place parentheses around the assignment to silence this warning
while (queryAtom = indigoNext(queryAtomIter))
^
( )
smindigo.cpp:73:30: note: use '==' to turn this assignment into an equality comparison
while (queryAtom = indigoNext(queryAtomIter))
^
==
smindigo.cpp:100:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (match = indigoNext(matchIter)) {
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:100:22: note: place parentheses around the assignment to silence this warning
while (match = indigoNext(matchIter)) {
^
( )
smindigo.cpp:100:22: note: use '==' to turn this assignment into an equality comparison
while (match = indigoNext(matchIter)) {
^
==
smindigo.cpp:102:30: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (queryAtom = indigoNext(queryAtomIter))
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:102:30: note: place parentheses around the assignment to silence this warning
while (queryAtom = indigoNext(queryAtomIter))
^
( )
smindigo.cpp:102:30: note: use '==' to turn this assignment into an equality comparison
while (queryAtom = indigoNext(queryAtomIter))
^
==
smindigo.cpp:127:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (component = indigoNext(componentIter)) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:127:26: note: place parentheses around the assignment to silence this warning
while (component = indigoNext(componentIter)) {
^
( )
smindigo.cpp:127:26: note: use '==' to turn this assignment into an equality comparison
while (component = indigoNext(componentIter)) {
^
==
smindigo.cpp:126:9: warning: variable 'largestComponent' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if (componentIter != -1) {
^~~~~~~~~~~~~~~~~~~
smindigo.cpp:147:12: note: uninitialized use occurs here
return largestComponent;
^~~~~~~~~~~~~~~~
smindigo.cpp:126:5: note: remove the 'if' if its condition is always true
if (componentIter != -1) {
^~~~~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:122:51: note: initialize the variable 'largestComponent' to silence this warning
int componentIter, component, largestComponent; // Indigo objects that require freeing
^
= 0
smindigo.cpp:155:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(atom = indigoNext(atomIter)) {
~~~~~^~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:155:16: note: place parentheses around the assignment to silence this warning
while(atom = indigoNext(atomIter)) {
^
( )
smindigo.cpp:155:16: note: use '==' to turn this assignment into an equality comparison
while(atom = indigoNext(atomIter)) {
^
==
smindigo.cpp:184:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(bond = indigoNext(bondIter)) {
~~~~~^~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:184:16: note: place parentheses around the assignment to silence this warning
while(bond = indigoNext(bondIter)) {
^
( )
smindigo.cpp:184:16: note: use '==' to turn this assignment into an equality comparison
while(bond = indigoNext(bondIter)) {
^
==
smindigo.cpp:203:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(atom = indigoNext(atomIter)) {
~~~~~^~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:203:16: note: place parentheses around the assignment to silence this warning
while(atom = indigoNext(atomIter)) {
^
( )
smindigo.cpp:203:16: note: use '==' to turn this assignment into an equality comparison
while(atom = indigoNext(atomIter)) {
^
==
smindigo.cpp:215:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(atom = indigoNext(atomIter)) {
~~~~~^~~~~~~~~~~~~~~~~~~~~~
smindigo.cpp:215:16: note: place parentheses around the assignment to silence this warning
while(atom = indigoNext(atomIter)) {
^
( )
smindigo.cpp:215:16: note: use '==' to turn this assignment into an equality comparison
while(atom = indigoNext(atomIter)) {
^
==
11 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o camb.so GetProperties.o fingerprint.o standardise.o misc.o smindigo.o -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/renderer -I/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/api/plugins/inchi -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.6/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.7/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.8/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.9/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.10/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Linux/x64/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Linux/x86/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Win/x64/lib -L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Win/x86/lib -lindigo-static -lcommon -lmolecule -lreaction -llayout -lz -ltinyxml -lgraph -lindigo-inchi-static -lindigo-renderer-static -lpng -lpixman -lcairo -linchi -lrender2d -lindigo-static -lcommon -lmolecule -lreaction -llayout -lz -ltinyxml -lgraph -lindigo-inchi-static -lindigo-renderer-static -lpng -lpixman -lcairo -linchi -lrender2d -lindigo-static -lcommon -lmolecule -lreaction -llayout -lz -ltinyxml -lgraph -lindigo-inchi-static -lindigo-renderer-static -lpng -lpixman -lcairo -linchi -lrender2d -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.6/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.7/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.8/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.9/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Mac/10.10/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Linux/x64/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Linux/x86/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Win/x64/lib'
ld: warning: directory not found for option '-L/private/var/folders/hb/cc7r8_7j7c55jqn7zqhhp_jh0000gs/T/RtmpQki79C/devtoolsb0a64c4d396a/cambDI-camb-ae439f1/camb/src/build/dist/Win/x86/lib'
ld: library not found for -lindigo-static
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [camb.so] Error 1
make: *** [all] Error 1
ERROR: compilation failed for package 'camb'
* removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/camb'
Error: Command failed (1)here is the session info();
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] car_2.1-2 rcdk_3.3.2 fingerprint_3.5.2
[4] XML_3.98-1.4 testthat_1.0.2 Rcpp_0.12.5
[7] devtools_1.11.1
loaded via a namespace (and not attached):
[1] nloptr_1.0.4 git2r_0.14.0 iterators_1.0.8
[4] tools_3.2.3 rcdklibs_1.5.8.4 digest_0.6.9
[7] lme4_1.1-12 memoise_1.0.0 nlme_3.1-128
[10] lattice_0.20-33 mgcv_1.8-9 png_0.1-7
[13] Matrix_1.2-3 curl_0.9.7 parallel_3.2.3
[16] SparseM_1.7 rJava_0.9-8 withr_1.0.1
[19] httr_1.1.0 MatrixModels_0.4-1 grid_3.2.3
[22] nnet_7.3-11 R6_2.1.2 minqa_1.2.4
[25] magrittr_1.5 MASS_7.3-45 splines_3.2.3
[28] pbkrtest_0.4-6 quantreg_5.24 crayon_1.3.1 
chepyle
Attempted camb installation gave the following error:
-- checking for module 'freetype2' -- package 'freetype2' not found
Installing FreeType2 (libfont-freetype-perl 0.03-1build4) did not not resolve the issue. Full error output is available as pdf file.