Rdisop 1.28.0
Steffen Neumann
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/Rdisop | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | [ OK ] | OK | OK | OK | |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rdisop
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
* installing *source* package ‘Rdisop’ ...
** 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 /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘Rdisop.Rnw’
** testing if installed package can be loaded
* DONE (Rdisop)