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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Rdisop_1.50.0.tar.gz && rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Rdisop_1.50.0.zip && rm Rdisop_1.50.0.tar.gz Rdisop_1.50.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 683k 100 683k 0 0 11.7M 0 --:--:-- --:--:-- --:--:-- 11.9M
install for i386
* installing *source* package 'Rdisop' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from disop.cpp:22:
./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 C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from disop.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from disop.cpp:26:
./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 C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from disop.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from disop.cpp:28:
./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 of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:43: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
~~~^~~~~~~~~~~~~~~
disop.cpp:239:68: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-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 of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~
disop.cpp:390:68: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:43: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:43: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~
disop.cpp:414:68: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-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;
^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/composedelement.cpp:8:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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])) ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rdisop.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/Rdisop.buildbin-libdir/00LOCK-Rdisop/00new/Rdisop/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rdisop'
finding HTML links ... done
addMolecules html
decomposeMass html
getMolecule html
initializeCHNOPS html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Rdisop' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from disop.cpp:22:
./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 C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from disop.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from disop.cpp:26:
./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 C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from disop.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from disop.cpp:28:
./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 of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:43: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
~~~^~~~~~~~~~~~~~~
disop.cpp:239:68: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-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 of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~
disop.cpp:390:68: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:43: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:43: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
~~~^~~~~~~~~~~~~~~
disop.cpp:414:68: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-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;
^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/composedelement.cpp:8:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from imslib/src/ims/composedelement.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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])) ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/matchmatrix.h:4,
from imslib/src/ims/calib/matchmatrix.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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,
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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13,
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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7,
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 of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
~~^~~~~~~~~~~~~~~~~~~~~
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4,
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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./imslib/src/ims/composedelement.h:6,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rdisop.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rdisop' as Rdisop_1.50.0.zip
* DONE (Rdisop)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Rdisop' successfully unpacked and MD5 sums checked
|
Rdisop.Rcheck/tests_i386/doRUnit.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "Rdisop" # <-- Change to package name!
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ path <- system.file(package=pkg, "unitTests")
+ }
+ cat("\nRunning unit tests\n")
+ print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+
+ library(package=pkg, character.only=TRUE)
+ ## attr(faahko, "filepaths") <- sapply(as.list(basename(attr(faahko, "filepaths"))),
+ ## function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT" ,x, package = "faahKO"))
+
+ ## If desired, load the name space to allow testing of private functions
+ ## if (is.element(pkg, loadedNamespaces()))
+ ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+ ##
+ ## or simply call PKG:::myPrivateFunction() in tests
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=paste(pathReport, "Summary.txt", sep=""))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=paste(pathReport, ".txt", sep=""))
+
+ ## Report to HTML file
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$nFail > 0 | tmp$nErr > 0) {
+ stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+ ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning("cannot run unit tests -- package RUnit is not available")
+ }
Running unit tests
$pkg
[1] "Rdisop"
$getwd
[1] "C:/Users/biocbuild/bbs-3.12-bioc/meat/Rdisop.Rcheck/tests_i386"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rdisop/unitTests"
Loading required package: Rcpp
Executing test function test.addformula1 ... done successfully.
Executing test function test.addformula2 ... done successfully.
Executing test function test.subformula1 ... done successfully.
Executing test function test.subformula2 ... done successfully.
Executing test function test.cid24892761 ... done successfully.
Executing test function test.cid46173807 ... done successfully.
Executing test function test.empty ... done successfully.
Executing test function test.exact ... done successfully.
Executing test function test.remove ... done successfully.
Executing test function test.minmaxElements1 ... done successfully.
Executing test function test.minmaxElements2 ... done successfully.
Executing test function test.minmaxElements3 ... done successfully.
Executing test function test.minmaxElements4 ... done successfully.
Executing test function test.minmaxElements5 ... done successfully.
Executing test function test.minmaxElements6 ... done successfully.
Executing test function test.minmaxElements7 ... done successfully.
Executing test function test.monoisotopicMasses ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Thu May 06 06:03:22 2021
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rdisop unit testing - 17 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
0.59 0.10 0.68
|
Rdisop.Rcheck/tests_x64/doRUnit.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "Rdisop" # <-- Change to package name!
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ path <- system.file(package=pkg, "unitTests")
+ }
+ cat("\nRunning unit tests\n")
+ print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+
+ library(package=pkg, character.only=TRUE)
+ ## attr(faahko, "filepaths") <- sapply(as.list(basename(attr(faahko, "filepaths"))),
+ ## function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT" ,x, package = "faahKO"))
+
+ ## If desired, load the name space to allow testing of private functions
+ ## if (is.element(pkg, loadedNamespaces()))
+ ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+ ##
+ ## or simply call PKG:::myPrivateFunction() in tests
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=paste(pathReport, "Summary.txt", sep=""))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=paste(pathReport, ".txt", sep=""))
+
+ ## Report to HTML file
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$nFail > 0 | tmp$nErr > 0) {
+ stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+ ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning("cannot run unit tests -- package RUnit is not available")
+ }
Running unit tests
$pkg
[1] "Rdisop"
$getwd
[1] "C:/Users/biocbuild/bbs-3.12-bioc/meat/Rdisop.Rcheck/tests_x64"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rdisop/unitTests"
Loading required package: Rcpp
Executing test function test.addformula1 ... done successfully.
Executing test function test.addformula2 ... done successfully.
Executing test function test.subformula1 ... done successfully.
Executing test function test.subformula2 ... done successfully.
Executing test function test.cid24892761 ... done successfully.
Executing test function test.cid46173807 ... done successfully.
Executing test function test.empty ... done successfully.
Executing test function test.exact ... done successfully.
Executing test function test.remove ... done successfully.
Executing test function test.minmaxElements1 ... done successfully.
Executing test function test.minmaxElements2 ... done successfully.
Executing test function test.minmaxElements3 ... done successfully.
Executing test function test.minmaxElements4 ... done successfully.
Executing test function test.minmaxElements5 ... done successfully.
Executing test function test.minmaxElements6 ... done successfully.
Executing test function test.minmaxElements7 ... done successfully.
Executing test function test.monoisotopicMasses ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Thu May 06 06:03:23 2021
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rdisop unit testing - 17 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
0.50 0.12 0.62
|
