Rdisop 1.33.0
Steffen Neumann
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rdisop_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Rdisop.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.33.0’
* 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 5.1Mb
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 sizes of PDF files under ‘inst/doc’ ... OK
* 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-3.4-bioc/meat/Rdisop.Rcheck/00check.log’
for details.
* installing *source* package ‘Rdisop’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:53:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.4-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-3.4-bioc/R/include/Rinternals.h:448:25: 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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-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-3.4-bioc/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/home/biocbuild/bbs-3.4-bioc/R/library/RcppClassic/lib -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)