Package: Rdisop

Version: 1.42.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Rdisop.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Rdisop_1.42.1.tar.gz

StartedAt: 2019-04-16 02:28:48 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:29:11 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 22.8 seconds

RetCode: 0

Status:  OK

CheckDir: Rdisop.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Rdisop.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Rdisop_1.42.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Rdisop.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.42.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/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. 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’
 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-3.8-bioc/meat/Rdisop.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Rdisop
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Rdisop’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:64:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/Rinternals.h:478:25: 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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/lib -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (Rdisop)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] "/home/biocbuild/bbs-3.8-bioc/meat/Rdisop.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.8-bioc/R/library/Rdisop/unitTests"

Loading required package: RcppClassic


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.monoisotopicMasses  ...  done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr 16 02:29:06 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rdisop unit testing - 10 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  0.564   0.036   0.714 

name	user	system	elapsed
addMolecules	0.004	0.000	0.004
decomposeMass	0.008	0.004	0.013
getMolecule	0.004	0.000	0.001
initializeCHNOPS	0.000	0.000	0.002