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### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Rdisop.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Rdisop_1.69.2.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Rdisop.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.69.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rdisop’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette without corresponding tangle output:
  ‘Rdisop.Rmd’
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Rdisop.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL Rdisop
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘Rdisop’ ...
** this is package ‘Rdisop’ version ‘1.69.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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:92:60: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
   92 |         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]
  106 |   bool parityeven = !parityodd;
      |        ^~~~~~~~~~
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:229:50: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  229 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:232:50: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  232 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:240:53: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  240 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:240:75: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  240 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:192:13: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable]
  192 |         int number_molecules_shown = 100;
      |             ^~~~~~~~~~~~~~~~~~~~~~
disop.cpp:170:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
  170 |     typedef distribution_t::mass_type mass_type;
      |                                       ^~~~~~~~~
disop.cpp:172:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs]
  172 |     typedef distribution_t::nominal_mass_type nominal_mass_type;
      |                                               ^~~~~~~~~~~~~~~~~
disop.cpp:175:42: warning: typedef ‘decomposition_type’ locally defined but not used [-Wunused-local-typedefs]
  175 |     typedef decompositions_t::value_type decomposition_type;
      |                                          ^~~~~~~~~~~~~~~~~~
disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:391:53: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  391 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:391:75: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  391 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:408:50: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  408 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:411:50: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  411 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:415:53: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  415 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:415:75: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  415 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:378:43: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
  378 |         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:627:43: warning: typedef ‘scorer_type’ locally defined but not used [-Wunused-local-typedefs]
  627 |     typedef DistributionProbabilityScorer scorer_type;
      |                                           ^~~~~~~~~~~
disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’:
disop.cpp:710:39: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
  710 |         typedef alphabet_t::container elements_type;
      |                                       ^~~~~~~~~~~~~
disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’:
disop.cpp:815:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
  815 |   typedef alphabet_t::container elements_type;
      |                                 ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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 ims::AbstractMoleculeSequenceParser::sequence_type&)’:
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:39: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   53 |         for (;  letter_pos < last_pos &&
      |                 ~~~~~~~~~~~~~~~~~~~~~~^~
   54 |                         ( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) ||
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./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:92:60: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
   92 |         typedef typename DecompositionWeights::weight_type weight_type;
      |                                                            ^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall -Werror=format-security  -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(size_type) const’:
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -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
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/00LOCK-Rdisop/00new/Rdisop/libs
** R
** data
*** moving datasets to lazyload DB
** 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)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(Rdisop)
Loading required package: Rcpp
> 
> testthat::test_check("Rdisop")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
  1.052   0.158   1.195