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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL scPipe
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Gene.cpp -o Gene.o
Gene.cpp: In member function ‘void Gene::flatten_exon()’:
Gene.cpp:105:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Interval>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
105 | for (auto i = 1; i < exon_vec.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
Gene.cpp: In function ‘std::ostream& operator<<(std::ostream&, const Gene&)’:
Gene.cpp:130:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Interval>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
130 | for (int i = 0; i < obj.exon_vec.size(); ++i)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c cellbarcode.cpp -o cellbarcode.o
cellbarcode.cpp: In member function ‘std::string Barcode::get_closest_match(const string&, int)’:
cellbarcode.cpp:77:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
77 | for (int i = 0; i < barcode_list.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
cellbarcode.cpp:82:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
82 | for (int i = 0; i < hamming_dists.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c parsebam.cpp -o parsebam.o
parsebam.cpp: In member function ‘int Bamdemultiplex::clean_bam_barcode(std::string, std::string, int, int)’:
parsebam.cpp:78:9: warning: variable ‘hts_retcode’ set but not used [-Wunused-but-set-variable]
78 | int hts_retcode;
| ^~~~~~~~~~~
parsebam.cpp:116:9: warning: unused variable ‘map_status’ [-Wunused-variable]
116 | int map_status;
| ^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c parsecount.cpp -o parsecount.o
parsecount.cpp: In function ‘void write_stat(std::string, std::string, std::vector<int>, std::unordered_map<std::__cxx11::basic_string<char>, UMI_dedup_stat>)’:
parsecount.cpp:266:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
266 | for (int i=0; i<UMI_dup_count.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:7:
transcriptmapping.h: In member function ‘void GeneBin::add_gene(Gene)’:
transcriptmapping.h:42:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} [-Wsign-compare]
42 | if (gene.st < start)
| ~~~~~~~~^~~~~~~
transcriptmapping.h:46:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} [-Wsign-compare]
46 | if (gene.en > end)
| ~~~~~~~~^~~~~
transcriptmapping.h: In member function ‘const bool GeneBin::overlaps(const Interval&)’:
transcriptmapping.h:54:24: warning: comparison of integer expressions of different signedness: ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
54 | return !(start > it.en) && !(end < it.st);
| ~~~~~~^~~~~~~
transcriptmapping.h:54:42: warning: comparison of integer expressions of different signedness: ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
54 | return !(start > it.en) && !(end < it.st);
| ~~~~^~~~~~~
In file included from config_hts.h:8,
from trimbarcode.h:6,
from rcpp_scPipe_func.cpp:3:
trimbarcode.h: At global scope:
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
190 | SCOPE int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: note: in definition of macro ‘__KSEQ_READ’
190 | SCOPE int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
| ^~~~~~~~~~
trimbarcode.h:11:1: note: in expansion of macro ‘KSEQ_INIT’
11 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: ‘void kseq_destroy(kseq_t*)’ defined but not used [-Wunused-function]
176 | SCOPE void kseq_destroy(kseq_t *ks) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: note: in definition of macro ‘__KSEQ_BASIC’
176 | SCOPE void kseq_destroy(kseq_t *ks) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
| ^~~~~~~~~~
trimbarcode.h:11:1: note: in expansion of macro ‘KSEQ_INIT’
11 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
170 | SCOPE kseq_t *kseq_init(type_t fd) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: in definition of macro ‘__KSEQ_BASIC’
170 | SCOPE kseq_t *kseq_init(type_t fd) \
| ^~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’
244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
| ^~~~~~~~~~
trimbarcode.h:11:1: note: in expansion of macro ‘KSEQ_INIT’
11 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-cpp.cpp -o test-cpp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c transcriptmapping.cpp -o transcriptmapping.o
In file included from transcriptmapping.cpp:2:
transcriptmapping.h: In member function ‘void GeneBin::add_gene(Gene)’:
transcriptmapping.h:42:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} [-Wsign-compare]
42 | if (gene.st < start)
| ~~~~~~~~^~~~~~~
transcriptmapping.h:46:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} [-Wsign-compare]
46 | if (gene.en > end)
| ~~~~~~~~^~~~~
transcriptmapping.h: In member function ‘const bool GeneBin::overlaps(const Interval&)’:
transcriptmapping.h:54:24: warning: comparison of integer expressions of different signedness: ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
54 | return !(start > it.en) && !(end < it.st);
| ~~~~~~^~~~~~~
transcriptmapping.h:54:42: warning: comparison of integer expressions of different signedness: ‘GeneBin::ull_int’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
54 | return !(start > it.en) && !(end < it.st);
| ~~~~^~~~~~~
transcriptmapping.cpp: In member function ‘int Mapping::map_exon(bam_hdr_t*, bam1_t*, std::string&, bool)’:
transcriptmapping.cpp:533:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
533 | for (int c=0; c<b->core.n_cigar; c++)
| ~^~~~~~~~~~~~~~~~
transcriptmapping.cpp: In member function ‘void Mapping::parse_align_warpper(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::string, bool, std::string, std::string, std::string, std::string, int, int, int)’:
transcriptmapping.cpp:678:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
678 | for (int i=1;i<fn_vec.size();i++)
| ~^~~~~~~~~~~~~~
transcriptmapping.cpp:686:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
686 | for (int i=1;i<fn_vec.size();i++)
| ~^~~~~~~~~~~~~~
transcriptmapping.cpp: In function ‘std::pair<int, int> {anonymous}::get_bc_umi_lengths(std::string)’:
transcriptmapping.cpp:701:20: warning: unused variable ‘bam_hdr’ [-Wunused-variable]
701 | bam_hdr_t *bam_hdr = bam_hdr_read(fp);
| ^~~~~~~
transcriptmapping.cpp: In member function ‘void Mapping::parse_align(std::string, std::string, bool, std::string, std::string, std::string, std::string, int, std::string, std::string, int, int)’:
transcriptmapping.cpp:755:9: warning: variable ‘hts_retcode’ set but not used [-Wunused-but-set-variable]
755 | int hts_retcode;
| ^~~~~~~~~~~
transcriptmapping.cpp: At global scope:
transcriptmapping.cpp:699:25: warning: ‘std::pair<int, int> {anonymous}::get_bc_umi_lengths(std::string)’ defined but not used [-Wunused-function]
699 | std::pair<int, int> get_bc_umi_lengths(string bam_fn) {
| ^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function ‘void kseq_t_to_bam_t(kseq_t*, bam1_t*, int)’:
trimbarcode.cpp:38:19: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
38 | if (b->m_data < b->l_data)
| ~~~~~~~~~~^~~~~~~~~~~
trimbarcode.cpp: In function ‘void paired_fastq_to_bam(char*, char*, char*, read_s, filter_s)’:
trimbarcode.cpp:92:9: warning: variable ‘hts_retcode’ set but not used [-Wunused-but-set-variable]
92 | int hts_retcode;
| ^~~~~~~~~~~
trimbarcode.cpp: In function ‘void paired_fastq_to_fastq(char*, char*, char*, read_s, filter_s, bool)’:
trimbarcode.cpp:450:24: warning: ‘o_stream_gz’ may be used uninitialized in this function [-Wmaybe-uninitialized]
450 | fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o scPipe.so Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o test-cpp.o test-runner.o transcriptmapping.o trimbarcode.o utils.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-scPipe/00new/scPipe/libs
** R
** data
** 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 (scPipe)
