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BioC 3.6: INSTALL report for Rdisop on veracruz1

This page was generated on 2017-08-16 13:39:55 -0400 (Wed, 16 Aug 2017).

Package 1100/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.37.0
Steffen Neumann
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rdisop
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rdisop
StartedAt: 2017-08-15 17:59:41 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:00:22 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 40.9 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### 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:159:39: warning: unused typedef 'mass_type' [-Wunused-local-typedef]
    typedef distribution_t::mass_type mass_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: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
   ‘Rdisop.Rnw’ 
** testing if installed package can be loaded
* DONE (Rdisop)