Rdisop 1.46.0
Steffen Neumann
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rdisop |
| Branch: RELEASE_3_10 |
| Last Commit: fdd73a9 |
| Last Changed Date: 2019-10-29 13:07:53 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Rdisop
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Rdisop’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from disop.cpp:18:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from disop.cpp:22:0:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:58: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from disop.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from disop.cpp:26:0:
./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<integer_decomposer_type> decomposer;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from disop.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from disop.cpp:28:0:
./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
typedef typename DecompositionWeights::weight_type weight_type;
^~~~~~~~~~~
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:106:8: warning: unused variable ‘parityeven’ [-Wunused-variable]
bool parityeven = !parityodd;
^~~~~~~~~~
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:228:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
~~~^~~~~~~~~~~~~~~
disop.cpp:239:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:191:6: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable]
int number_molecules_shown = 100;
^~~~~~~~~~~~~~~~~~~~~~
disop.cpp:169:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::mass_type mass_type;
^~~~~~~~~
disop.cpp:171:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::nominal_mass_type nominal_mass_type;
^~~~~~~~~~~~~~~~~
disop.cpp:174:42: warning: typedef ‘decomposition_type’ locally defined but not used [-Wunused-local-typedefs]
typedef decompositions_t::value_type decomposition_type;
^~~~~~~~~~~~~~~~~~
disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:390:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~
disop.cpp:390:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~
disop.cpp:414:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:377:40: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::mass_type mass_type;
^~~~~~~~~
disop.cpp: In function ‘SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)’:
disop.cpp:626:43: warning: typedef ‘scorer_type’ locally defined but not used [-Wunused-local-typedefs]
typedef DistributionProbabilityScorer scorer_type;
^~~~~~~~~~~
disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’:
disop.cpp:709:32: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
typedef alphabet_t::container elements_type;
^~~~~~~~~~~~~
disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’:
disop.cpp:814:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
typedef alphabet_t::container elements_type;
^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/composedelement.cpp:8:0:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:58: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/composedelement.cpp: In constructor ‘ims::ComposedElement::ComposedElement(const name_type&, const ims::Alphabet&, unsigned int)’:
imslib/src/ims/composedelement.cpp:26:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<sequence_parser_type> parser;
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/composedelement.cpp:28:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/composedelement.cpp:30:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/composedelement.cpp: At global scope:
imslib/src/ims/composedelement.cpp:116:73: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/distributedalphabet.h:7,
from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function ‘virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)’:
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
for (; letter_pos < last_pos &&
~~~~~~~~~~~~~~~~~~~~~~^~
( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:0:
./imslib/src/ims/calib/matchmatrix.h:61:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > countMatches();
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:0:
./imslib/src/ims/calib/matchmatrix.h:65:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > MatchMatrix::countMatches() {
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: In member function ‘std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatches()’:
imslib/src/ims/calib/matchmatrix.cpp:82:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: At global scope:
imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: In member function ‘std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatchesRestrictive()’:
imslib/src/ims/calib/matchmatrix.cpp:103:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13:0,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/matchmatrix.h:61:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > countMatches();
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13:0,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/matchmatrix.h:65:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h:146:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > getMapping() const;
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h:169:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > mapping;
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function ‘void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector<ims::RepresentativeScale>&, int, int, float)’:
./imslib/src/ims/calib/linearpointsetmatcher.h:281:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > mapping(0);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function ‘int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)’:
./imslib/src/ims/calib/linearpointsetmatcher.h:324:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h:326:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
results.mapping = std::auto_ptr<std::map<int,int> >(0);
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope:
imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function ‘std::auto_ptr<std::map<int, int> > ims::LinearPointSetMatcher::getMapping() const’:
imslib/src/ims/calib/linearpointsetmatcher.cpp:86:15: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:15: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:0:
./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<integer_decomposer_type> decomposer;
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/decomp/decomputils.h:12,
from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:0:
./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
typedef typename DecompositionWeights::weight_type weight_type;
^~~~~~~~~~~
imslib/src/ims/decomp/realmassdecomposer.cpp: In constructor ‘ims::RealMassDecomposer::RealMassDecomposer(const ims::Weights&)’:
imslib/src/ims/decomp/realmassdecomposer.cpp:21:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
decomposer = std::auto_ptr<integer_decomposer_type>(
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/characteralphabet.h:6,
from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4:0,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:58: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from ./imslib/src/ims/composedelement.h:6,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/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 -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-Rdisop/00new/Rdisop/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rdisop)