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BioC 3.5: CHECK report for Rdisop on malbec2

This page was generated on 2017-08-16 13:13:00 -0400 (Wed, 16 Aug 2017).

Package 1084/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.36.0
Steffen Neumann
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Rdisop
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rdisop
Version: 1.36.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rdisop_1.36.0.tar.gz
StartedAt: 2017-08-16 01:42:18 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:42:59 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 41.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Rdisop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rdisop_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Rdisop.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.36.0’
* 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
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
* 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 R 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘RcppClassic’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 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 compiled code ... NOTE
File ‘Rdisop/libs/Rdisop.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘imslib/src/ims/utils/distribution.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/Rdisop.Rcheck/00check.log’
for details.


Rdisop.Rcheck/00install.out:

* installing *source* package ‘Rdisop’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from disop.cpp:18:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
In file included from disop.cpp:28:0:
./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename DecompositionWeights::weight_type weight_type;
                                                     ^
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:106:8: warning: unused variable ‘parityeven’ [-Wunused-variable]
   bool parityeven = !parityodd;
        ^
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:218:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:221:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:229:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
                                              ^
disop.cpp:229:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
                                                                    ^
disop.cpp:181:6: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable]
  int number_molecules_shown = 100;
      ^
disop.cpp:159:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
     typedef distribution_t::mass_type mass_type;
                                       ^
disop.cpp:161:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs]
     typedef distribution_t::nominal_mass_type nominal_mass_type;
                                               ^
disop.cpp:164:42: 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:378:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                              ^
disop.cpp:378:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                                                    ^
disop.cpp:395:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:398:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:402:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                              ^
disop.cpp:402:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                                                    ^
disop.cpp:365:40: 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:623:43: 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:712:32: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
  typedef alphabet_t::container elements_type;
                                ^
In file included from /home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:53:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include/RcppClassic.h:27,
                 from disop.cpp:33:
disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’:
disop.cpp:825:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
     const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));
                                                                 ^
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:463:25: note: in definition of macro ‘CHAR’
 #define CHAR(x)  R_CHAR(x)
                         ^
disop.cpp:827:86: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
     nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];
                                                                                      ^
disop.cpp:829:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
     SEXP isotope = getListElement(l, "isotope"); 
                                               ^
disop.cpp:831:63: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
     int numisotopes = Rf_length(getListElement(isotope, "mass"));
                                                               ^
disop.cpp:832:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
     double *mass = REAL(getListElement(isotope, "mass")); 
                                                       ^
disop.cpp:833:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
     double *abundance = REAL(getListElement(isotope, "abundance")); 
                                                                 ^
disop.cpp:817:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef alphabet_t::container elements_type;
                                 ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
                 from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/distributedalphabet.h:7,
                 from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function ‘virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)’:
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  for (; letter_pos < last_pos && 
                               ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/decomp/decomputils.h:12,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:0:
./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename DecompositionWeights::weight_type weight_type;
                                                     ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/characteralphabet.h:6,
                 from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
                 from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
g++ -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/home/biocbuild/bbs-3.5-bioc/R/library/RcppClassic/lib -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/Rdisop.Rcheck/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rdisop)

Rdisop.Rcheck/Rdisop-Ex.timings:

nameusersystemelapsed
addMolecules0.0000.0040.003
decomposeMass0.2160.0040.218
getMolecule0.0040.0000.001
initializeCHNOPS0.0000.0000.001