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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1694/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.66.0  (landing page)
Steffen Neumann
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/Rdisop
git_branch: RELEASE_3_20
git_last_commit: f99f401
git_last_commit_date: 2024-10-29 09:28:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Rdisop on nebbiolo2

To the developers/maintainers of the Rdisop package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rdisop.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rdisop
Version: 1.66.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rdisop.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rdisop_1.66.0.tar.gz
StartedAt: 2024-12-20 04:37:28 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:37:49 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 21.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Rdisop.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rdisop.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rdisop_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rdisop.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.66.0’
* 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 ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
* checking package directory ... OK
* checking ‘build’ 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 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
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/Rdisop/libs/Rdisop.so’:
  Found ‘rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
  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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Rdisop.Rcheck/00check.log’
for details.


Installation output

Rdisop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rdisop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Rdisop’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 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:228:50: 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]
  228 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:50: 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]
  231 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:53: 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]
  239 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:239:75: 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]
  239 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:191:13: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable]
  191 |         int number_molecules_shown = 100;
      |             ^~~~~~~~~~~~~~~~~~~~~~
disop.cpp:169:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
  169 |     typedef distribution_t::mass_type mass_type;
      |                                       ^~~~~~~~~
disop.cpp:171:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs]
  171 |     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]
  174 |     typedef decompositions_t::value_type decomposition_type;
      |                                          ^~~~~~~~~~~~~~~~~~
disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:390:53: 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]
  390 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:390:75: 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]
  390 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:50: 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]
  407 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:50: 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]
  410 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:53: 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]
  414 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:414:75: 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]
  414 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:377:43: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
  377 |         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]
  626 |     typedef DistributionProbabilityScorer scorer_type;
      |                                           ^~~~~~~~~~~
disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’:
disop.cpp:709:39: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
  709 |         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]
  814 |   typedef alphabet_t::container elements_type;
      |                                 ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:
./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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7,
                 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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function ‘virtual void ims::KeggLigandCompoundsParser::parse(const 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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 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/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -I./imslib/src/ -fpic  -g -O2  -Wall  -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7,
                 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/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rdisop/00new/Rdisop/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rdisop)

Tests output

Rdisop.Rcheck/tests/doRUnit.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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] "/home/biocbuild/bbs-3.20-bioc/meat/Rdisop.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpcEzO6s/RLIBS_5b4672e1e79fa/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  ... You specified a charge z different from 0. Please read the details part of the documentation.
 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 -- Fri Dec 20 04:37:43 2024 
*********************************************** 
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
Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
7: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
8: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
9: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
10: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
> 
> proc.time()
   user  system elapsed 
  0.401   0.085   0.474 

Rdisop.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # 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
> 
> test_check("Rdisop")
You specified a charge z different from 0. Please read the details part of the documentation.
You specified a charge z different from 0. Please read the details part of the documentation.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
  0.741   0.078   0.809 

Example timings

Rdisop.Rcheck/Rdisop-Ex.timings

nameusersystemelapsed
addMolecules0.0020.0000.002
decomposeIsotopes0.0080.0030.012
getMolecule0.0010.0000.001
initializeElements0.0020.0010.002