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This page was generated on 2018-04-12 13:32:33 -0400 (Thu, 12 Apr 2018).
Package 1143/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Rdisop 1.38.0 Steffen Neumann
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | [ ERROR ] | ERROR | skipped | skipped |
Package: Rdisop |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rdisop |
StartedAt: 2018-04-11 17:58:48 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 17:59:31 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 42.3 seconds |
RetCode: 1 |
Status: ERROR |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rdisop ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ * installing *source* package ‘Rdisop’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"))); ^ 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")); ^ In file included from disop.cpp:28: ./imslib/src/ims/decomp/decomputils.h:92:53: warning: unused typedef 'weight_type' [-Wunused-local-typedef] typedef typename DecompositionWeights::weight_type weight_type; ^ disop.cpp:164:42: warning: unused typedef 'decomposition_type' [-Wunused-local-typedef] typedef decompositions_t::value_type decomposition_type; ^ disop.cpp:161:47: warning: unused typedef 'nominal_mass_type' [-Wunused-local-typedef] typedef distribution_t::nominal_mass_type nominal_mass_type; ^ disop.cpp:159:39: warning: unused typedef 'mass_type' [-Wunused-local-typedef] typedef distribution_t::mass_type mass_type; ^ disop.cpp:365:40: warning: unused typedef 'mass_type' [-Wunused-local-typedef] typedef distribution_t::mass_type mass_type; ^ disop.cpp:623:43: warning: unused typedef 'scorer_type' [-Wunused-local-typedef] typedef DistributionProbabilityScorer scorer_type; ^ disop.cpp:712:32: warning: unused typedef 'elements_type' [-Wunused-local-typedef] typedef alphabet_t::container elements_type; ^ disop.cpp:817:33: warning: unused typedef 'elements_type' [-Wunused-local-typedef] typedef alphabet_t::container elements_type; ^ 16 warnings generated. clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9: ./imslib/src/ims/decomp/decomputils.h:92:53: warning: unused typedef 'weight_type' [-Wunused-local-typedef] typedef typename DecompositionWeights::weight_type weight_type; ^ 1 warning generated. clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -g -O2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fPIC -Wall -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/3.4/Resources/library/RcppClassic/lib/libRcppClassic.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/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 sh: line 1: 40217 Abort trap: 6 '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpDjMCy4/file87f07babb193' R(40217,0x7fff7acb1000) malloc: *** error for object 0x7fff7e6f3c30: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rdisop’