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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ORFik
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘void calc_z(const string&, vi&)’:
findORFsHelpers.cpp:57:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
       for (z[i] = r - i; r < len; ++r, ++z[i])
       ^~~
findORFsHelpers.cpp:60:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
         --r;
         ^~
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)’:
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < uorfSize/2; i++) {
                   ~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function ‘Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)’:
pmapFromTranscripts.cpp:151:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){
                  ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function ‘void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:22:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:68:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)’:
pmapToTranscripts.cpp:126:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){ // Width per exon in x
                  ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 1; i < 2 * xSize; i = i + 2) {
                    ~~^~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-ORFik/00new/ORFik/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 (ORFik)