Rdisop 1.30.0
Steffen Neumann
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rdisop | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | [ OK ] | |
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###
### Running command:
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### rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rdisop_1.30.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rdisop.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rdisop.buildbin-libdir Rdisop_1.30.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rdisop’ ...
Makefile:1270: examples/.deps/peaklist.Po: No such file or directory
Makefile:1271: src/ims/.deps/alphabet.Plo: No such file or directory
Makefile:1272: src/ims/.deps/characteralphabet.Plo: No such file or directory
Makefile:1273: src/ims/.deps/composedelement.Plo: No such file or directory
Makefile:1274: src/ims/.deps/distributedalphabet.Plo: No such file or directory
Makefile:1275: src/ims/.deps/distributionprobabilityscorer.Plo: No such file or directory
Makefile:1276: src/ims/.deps/element.Plo: No such file or directory
Makefile:1277: src/ims/.deps/isotopedistribution.Plo: No such file or directory
Makefile:1278: src/ims/.deps/isotopespecies.Plo: No such file or directory
Makefile:1279: src/ims/.deps/nitrogenrulefilter.Plo: No such file or directory
Makefile:1280: src/ims/.deps/transformation.Plo: No such file or directory
Makefile:1281: src/ims/.deps/weights.Plo: No such file or directory
Makefile:1282: src/ims/base/parser/.deps/alphabettextparser.Plo: No such file or directory
Makefile:1283: src/ims/base/parser/.deps/distributedalphabettextparser.Plo: No such file or directory
Makefile:1284: src/ims/base/parser/.deps/keggligandcompoundsparser.Plo: No such file or directory
Makefile:1285: src/ims/base/parser/.deps/massestextparser.Plo: No such file or directory
Makefile:1286: src/ims/base/parser/.deps/moleculeionchargemodificationparser.Plo: No such file or directory
Makefile:1287: src/ims/base/parser/.deps/moleculesequenceparser.Plo: No such file or directory
Makefile:1288: src/ims/base/parser/.deps/standardmoleculesequenceparser.Plo: No such file or directory
Makefile:1289: src/ims/calib/.deps/linearpointsetmatcher.Plo: No such file or directory
Makefile:1290: src/ims/calib/.deps/linepairstabber.Plo: No such file or directory
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Makefile:1297: tests/.deps/distributedalphabettest.Po: No such file or directory
Makefile:1298: tests/.deps/distributionprobabilityscorertest.Po: No such file or directory
Makefile:1299: tests/.deps/elementtest.Po: No such file or directory
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Makefile:1307: tests/.deps/markovsequencegeneratortest.Po: No such file or directory
Makefile:1308: tests/.deps/massintensitypeaktest.Po: No such file or directory
Makefile:1309: tests/.deps/massintensitytofpeaktest.Po: No such file or directory
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Makefile:1315: tests/.deps/polynomialtransformationtest.Po: No such file or directory
Makefile:1316: tests/.deps/randomsequencegeneratortest.Po: No such file or directory
Makefile:1317: tests/.deps/roundtest.Po: No such file or directory
Makefile:1318: tests/.deps/shifttransformationtest.Po: No such file or directory
Makefile:1319: tests/.deps/stopwatchtest.Po: No such file or directory
Makefile:1320: tests/.deps/tests.Po: No such file or directory
Makefile:1321: tests/.deps/tofpeaktest.Po: No such file or directory
Makefile:1322: tests/.deps/weightstest.Po: No such file or directory
Makefile:1323: tests/base/parser/.deps/massestextparsertest.Po: No such file or directory
Makefile:1324: tests/base/parser/.deps/moleculesequenceparsertest.Po: No such file or directory
Makefile:1325: tests/calib/.deps/linearpointsetmatchertest.Po: No such file or directory
Makefile:1326: tests/calib/.deps/linepairstabbertest.Po: No such file or directory
Makefile:1327: tests/calib/.deps/matchmatrixtest.Po: No such file or directory
Makefile:1328: tests/decomp/.deps/integermassdecomposertest.Po: No such file or directory
Makefile:1329: tests/decomp/.deps/realmassdecomposertest.Po: No such file or directory
Makefile:1330: tests/decomp/.deps/twomassdecomposer2test.Po: No such file or directory
Makefile:1331: tests/modifier/.deps/intensitynormalizermodifiertest.Po: No such file or directory
Makefile:1332: tests/modifier/.deps/massrangemodifiertest.Po: No such file or directory
Makefile:1333: tests/modifier/.deps/multimodifiertest.Po: No such file or directory
Makefile:1334: tests/modifier/.deps/shiftmodifiertest.Po: No such file or directory
Makefile:1335: tests/modifier/.deps/sortmodifiertest.Po: No such file or directory
Makefile:1336: tests/modifier/.deps/unificationmodifiertest.Po: No such file or directory
Makefile:1337: tests/modifier/.deps/voidmodifiertest.Po: No such file or directory
Makefile:1338: tools/.deps/decompvalidation.Po: No such file or directory
Makefile:1339: tools/.deps/elementalcompositions.Po: No such file or directory
Makefile:1340: tools/.deps/histogram.Po: No such file or directory
Makefile:1341: tools/.deps/imsdecomp.Po: No such file or directory
Makefile:1342: tools/.deps/imsfrag.Po: No such file or directory
Makefile:1343: tools/.deps/imsintdecomp.Po: No such file or directory
Makefile:1344: tools/.deps/keggruntimes.Po: No such file or directory
Makefile:1345: tools/.deps/numberdecompositions.Po: No such file or directory
Makefile:1346: tools/.deps/options.Po: No such file or directory
Makefile:1347: tools/.deps/peaklistvalidation.Po: No such file or directory
Makefile:1348: tools/.deps/scoredecompositions.Po: No such file or directory
make: *** No rule to make target `tools/.deps/scoredecompositions.Po'.
make: *** No rule to make target `tools/.deps/peaklistvalidation.Po'.
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make: *** No rule to make target `examples/.deps/peaklist.Po'.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/edd/Rdisop/Rdisop/src/imslib/config/missing --run autoconf
/bin/bash: /home/edd/Rdisop/Rdisop/src/imslib/config/missing: No such file or directory
make: *** [configure] Error 127
make: Failed to remake makefile `tools/.deps/scoredecompositions.Po'.
make: Failed to remake makefile `tools/.deps/peaklistvalidation.Po'.
make: Failed to remake makefile `tools/.deps/options.Po'.
make: Failed to remake makefile `tools/.deps/numberdecompositions.Po'.
make: Failed to remake makefile `tools/.deps/keggruntimes.Po'.
make: Failed to remake makefile `tools/.deps/imsintdecomp.Po'.
make: Failed to remake makefile `tools/.deps/imsfrag.Po'.
make: Failed to remake makefile `tools/.deps/imsdecomp.Po'.
make: Failed to remake makefile `tools/.deps/histogram.Po'.
make: Failed to remake makefile `tools/.deps/elementalcompositions.Po'.
make: Failed to remake makefile `tools/.deps/decompvalidation.Po'.
make: Failed to remake makefile `tests/modifier/.deps/voidmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/unificationmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/sortmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/shiftmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/multimodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/massrangemodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/intensitynormalizermodifiertest.Po'.
make: Failed to remake makefile `tests/decomp/.deps/twomassdecomposer2test.Po'.
make: Failed to remake makefile `tests/decomp/.deps/realmassdecomposertest.Po'.
make: Failed to remake makefile `tests/decomp/.deps/integermassdecomposertest.Po'.
make: Failed to remake makefile `tests/calib/.deps/matchmatrixtest.Po'.
make: Failed to remake makefile `tests/calib/.deps/linepairstabbertest.Po'.
make: Failed to remake makefile `tests/calib/.deps/linearpointsetmatchertest.Po'.
make: Failed to remake makefile `tests/base/parser/.deps/moleculesequenceparsertest.Po'.
make: Failed to remake makefile `tests/base/parser/.deps/massestextparsertest.Po'.
make: Failed to remake makefile `tests/.deps/weightstest.Po'.
make: Failed to remake makefile `tests/.deps/tofpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/tests.Po'.
make: Failed to remake makefile `tests/.deps/stopwatchtest.Po'.
make: Failed to remake makefile `tests/.deps/shifttransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/roundtest.Po'.
make: Failed to remake makefile `tests/.deps/randomsequencegeneratortest.Po'.
make: Failed to remake makefile `tests/.deps/polynomialtransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/pmffragmentertest.Po'.
make: Failed to remake makefile `tests/.deps/peakpropertyiteratortest.Po'.
make: Failed to remake makefile `tests/.deps/peaklisttest.Po'.
make: Failed to remake makefile `tests/.deps/masstofpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/masspeaktest.Po'.
make: Failed to remake makefile `tests/.deps/massintensitytofpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/massintensitypeaktest.Po'.
make: Failed to remake makefile `tests/.deps/markovsequencegeneratortest.Po'.
make: Failed to remake makefile `tests/.deps/lineartransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/isotopespeciestest.Po'.
make: Failed to remake makefile `tests/.deps/isotopedistributiontest.Po'.
make: Failed to remake makefile `tests/.deps/intensitypeaktest.Po'.
make: Failed to remake makefile `tests/.deps/identitytransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/fragmentpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/exceptiontest.Po'.
make: Failed to remake makefile `tests/.deps/elementtest.Po'.
make: Failed to remake makefile `tests/.deps/distributionprobabilityscorertest.Po'.
make: Failed to remake makefile `tests/.deps/distributedalphabettest.Po'.
make: Failed to remake makefile `tests/.deps/composedelementtest.Po'.
make: Failed to remake makefile `tests/.deps/chebyshevfittertest.Po'.
make: Failed to remake makefile `tests/.deps/alphabettest.Po'.
make: Failed to remake makefile `src/ims/utils/.deps/distribution.Plo'.
make: Failed to remake makefile `src/ims/decomp/.deps/realmassdecomposer.Plo'.
make: Failed to remake makefile `src/ims/calib/.deps/matchmatrix.Plo'.
make: Failed to remake makefile `src/ims/calib/.deps/linepairstabber.Plo'.
make: Failed to remake makefile `src/ims/calib/.deps/linearpointsetmatcher.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/standardmoleculesequenceparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/moleculesequenceparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/moleculeionchargemodificationparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/massestextparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/keggligandcompoundsparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/distributedalphabettextparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/alphabettextparser.Plo'.
make: Failed to remake makefile `src/ims/.deps/weights.Plo'.
make: Failed to remake makefile `src/ims/.deps/transformation.Plo'.
make: Failed to remake makefile `src/ims/.deps/nitrogenrulefilter.Plo'.
make: Failed to remake makefile `src/ims/.deps/isotopespecies.Plo'.
make: Failed to remake makefile `src/ims/.deps/isotopedistribution.Plo'.
make: Failed to remake makefile `src/ims/.deps/element.Plo'.
make: Failed to remake makefile `src/ims/.deps/distributionprobabilityscorer.Plo'.
make: Failed to remake makefile `src/ims/.deps/distributedalphabet.Plo'.
make: Failed to remake makefile `src/ims/.deps/composedelement.Plo'.
make: Failed to remake makefile `src/ims/.deps/characteralphabet.Plo'.
make: Failed to remake makefile `src/ims/.deps/alphabet.Plo'.
make: Failed to remake makefile `examples/.deps/peaklist.Po'.
make: Failed to remake makefile `Makefile'.
rm -f tools/scoredecompositions tools/peaklistvalidation tools/numberdecompositions tools/keggruntimes tools/imsfrag tools/imsdecomp tools/imsintdecomp tools/histogram tools/decompvalidation tools/imsdecompstatic tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
rm -rf .libs _libs
rm -rf examples/.libs examples/_libs
rm -rf src/.libs src/_libs
rm -rf src/ims/.libs src/ims/_libs
rm -rf src/ims/base/parser/.libs src/ims/base/parser/_libs
rm -rf src/ims/calib/.libs src/ims/calib/_libs
rm -rf src/ims/decomp/.libs src/ims/decomp/_libs
rm -rf src/ims/utils/.libs src/ims/utils/_libs
rm -rf tests/.libs tests/_libs
rm -rf tools/.libs tools/_libs
rm -f *.o
rm -f examples/peaklist.o
rm -f src/ims/alphabet.o
rm -f src/ims/alphabet.lo
rm -f src/ims/base/parser/alphabettextparser.o
rm -f src/ims/base/parser/alphabettextparser.lo
rm -f src/ims/base/parser/distributedalphabettextparser.o
rm -f src/ims/base/parser/distributedalphabettextparser.lo
rm -f src/ims/base/parser/keggligandcompoundsparser.o
rm -f src/ims/base/parser/keggligandcompoundsparser.lo
rm -f src/ims/base/parser/massestextparser.o
rm -f src/ims/base/parser/massestextparser.lo
rm -f src/ims/base/parser/moleculeionchargemodificationparser.o
rm -f src/ims/base/parser/moleculeionchargemodificationparser.lo
rm -f src/ims/base/parser/moleculesequenceparser.o
rm -f src/ims/base/parser/moleculesequenceparser.lo
rm -f src/ims/base/parser/standardmoleculesequenceparser.o
rm -f src/ims/base/parser/standardmoleculesequenceparser.lo
rm -f src/ims/calib/linearpointsetmatcher.o
rm -f src/ims/calib/linearpointsetmatcher.lo
rm -f src/ims/calib/linepairstabber.o
rm -f src/ims/calib/linepairstabber.lo
rm -f src/ims/calib/matchmatrix.o
rm -f src/ims/calib/matchmatrix.lo
rm -f src/ims/characteralphabet.o
rm -f src/ims/characteralphabet.lo
rm -f src/ims/composedelement.o
rm -f src/ims/composedelement.lo
rm -f src/ims/decomp/realmassdecomposer.o
rm -f src/ims/decomp/realmassdecomposer.lo
rm -f src/ims/distributedalphabet.o
rm -f src/ims/distributedalphabet.lo
rm -f src/ims/distributionprobabilityscorer.o
rm -f src/ims/distributionprobabilityscorer.lo
rm -f src/ims/element.o
rm -f src/ims/element.lo
rm -f src/ims/isotopedistribution.o
rm -f src/ims/isotopedistribution.lo
rm -f src/ims/isotopespecies.o
rm -f src/ims/isotopespecies.lo
rm -f src/ims/nitrogenrulefilter.o
rm -f src/ims/nitrogenrulefilter.lo
rm -f src/ims/transformation.o
rm -f src/ims/transformation.lo
rm -f src/ims/utils/distribution.o
rm -f src/ims/utils/distribution.lo
rm -f src/ims/weights.o
rm -f src/ims/weights.lo
rm -f tests/alphabettest.o
rm -f tests/base/parser/massestextparsertest.o
rm -f tests/base/parser/moleculesequenceparsertest.o
rm -f tests/calib/linearpointsetmatchertest.o
rm -f tests/calib/linepairstabbertest.o
rm -f tests/calib/matchmatrixtest.o
rm -f tests/chebyshevfittertest.o
rm -f tests/composedelementtest.o
rm -f tests/decomp/integermassdecomposertest.o
rm -f tests/decomp/realmassdecomposertest.o
rm -f tests/decomp/twomassdecomposer2test.o
rm -f tests/distributedalphabettest.o
rm -f tests/distributionprobabilityscorertest.o
rm -f tests/elementtest.o
rm -f tests/exceptiontest.o
rm -f tests/fragmentpeaktest.o
rm -f tests/identitytransformationtest.o
rm -f tests/intensitypeaktest.o
rm -f tests/isotopedistributiontest.o
rm -f tests/isotopespeciestest.o
rm -f tests/lineartransformationtest.o
rm -f tests/markovsequencegeneratortest.o
rm -f tests/massintensitypeaktest.o
rm -f tests/massintensitytofpeaktest.o
rm -f tests/masspeaktest.o
rm -f tests/masstofpeaktest.o
rm -f tests/modifier/intensitynormalizermodifiertest.o
rm -f tests/modifier/massrangemodifiertest.o
rm -f tests/modifier/multimodifiertest.o
rm -f tests/modifier/shiftmodifiertest.o
rm -f tests/modifier/sortmodifiertest.o
rm -f tests/modifier/unificationmodifiertest.o
rm -f tests/modifier/voidmodifiertest.o
rm -f tests/peaklisttest.o
rm -f tests/peakpropertyiteratortest.o
rm -f tests/pmffragmentertest.o
rm -f tests/polynomialtransformationtest.o
rm -f tests/randomsequencegeneratortest.o
rm -f tests/roundtest.o
rm -f tests/shifttransformationtest.o
rm -f tests/stopwatchtest.o
rm -f tests/tests.o
rm -f tests/tofpeaktest.o
rm -f tests/weightstest.o
rm -f tools/decompvalidation.o
rm -f tools/elementalcompositions.o
rm -f tools/histogram.o
rm -f tools/imsdecomp.o
rm -f tools/imsfrag.o
rm -f tools/imsintdecomp.o
rm -f tools/keggruntimes.o
rm -f tools/numberdecompositions.o
rm -f tools/options.o
rm -f tools/peaklistvalidation.o
rm -f tools/scoredecompositions.o
rm -f *.lo
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c disop.cpp -o disop.o
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
bool parityeven = !parityodd;
^
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
int number_molecules_shown = 100;
^
disop.cpp:825:59: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:440:25: note: expanded from macro 'CHAR'
#define CHAR(x) R_CHAR(x)
^
disop.cpp:827:80: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];
^
disop.cpp:829:38: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
SEXP isotope = getListElement(l, "isotope");
^
disop.cpp:831:57: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
int numisotopes = Rf_length(getListElement(isotope, "mass"));
^
disop.cpp:832:49: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
double *mass = REAL(getListElement(isotope, "mass"));
^
disop.cpp:833:54: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
double *abundance = REAL(getListElement(isotope, "abundance"));
^
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"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
for (; letter_pos < last_pos &&
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: note: place parentheses around the '&&' expression to silence this warning
for (; letter_pos < last_pos &&
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
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 Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o /Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppClassic/lib/libRcppClassic.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rdisop)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"