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INSTALL report for scPipe on tokay2

This page was generated on 2018-10-17 08:44:45 -0400 (Wed, 17 Oct 2018).

Package 1332/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPipe 1.2.1
Luyi Tian
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scPipe
Branch: RELEASE_3_7
Last Commit: 19a1726
Last Changed Date: 2018-05-31 19:42:56 -0400 (Thu, 31 May 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scPipe
Version: 1.2.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scPipe_1.2.1.tar.gz && rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scPipe.buildbin-libdir scPipe_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scPipe_1.2.1.zip && rm scPipe_1.2.1.tar.gz scPipe_1.2.1.zip
StartedAt: 2018-10-16 19:41:41 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:44:45 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 184.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scPipe_1.2.1.tar.gz && rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scPipe.buildbin-libdir scPipe_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scPipe_1.2.1.zip && rm scPipe_1.2.1.tar.gz scPipe_1.2.1.zip
###
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install for i386

* installing *source* package 'scPipe' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Gene.cpp -o Gene.o
Gene.cpp: In member function 'void Gene::flatten_exon()':
Gene.cpp:103:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 1; i < exon_vec.size(); i++)
                        ^
Gene.cpp: In function 'std::ostream& operator<<(std::ostream&, const Gene&)':
Gene.cpp:128:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < obj.exon_vec.size(); ++i)
                       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Interval.cpp -o Interval.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cellbarcode.cpp -o cellbarcode.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c detect_barcode.cpp -o detect_barcode.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c parsebam.cpp -o parsebam.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c parsecount.cpp -o parsecount.o
parsecount.cpp: In function 'void write_stat(std::string, std::string, std::vector<int>, std::unordered_map<std::basic_string<char>, UMI_dedup_stat>)':
parsecount.cpp:134:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<UMI_dup_count.size(); i++)
                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:7:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.st < start)
                     ^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.en > end)
                     ^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         return !(start > it.en) && !(end < it.st);
                        ^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         return !(start > it.en) && !(end < it.st);
                                          ^
In file included from config_hts.h:8:0,
                 from trimbarcode.h:6,
                 from rcpp_scPipe_func.cpp:3:
trimbarcode.h: At global scope:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:170:16: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
  SCOPE kseq_t *kseq_init(type_t fd)         \
                ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:176:13: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:190:12: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  SCOPE int kseq_read(kseq_t *seq) \
            ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
  __KSEQ_READ(SCOPE)
  ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c transcriptmapping.cpp -o transcriptmapping.o
In file included from transcriptmapping.cpp:2:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.st < start)
                     ^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.en > end)
                     ^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         return !(start > it.en) && !(end < it.st);
                        ^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         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:464:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int c=0; c<b->core.n_cigar; c++)
                    ^
transcriptmapping.cpp: In member function 'void Mapping::parse_align(std::string, std::string, bool, std::string, std::string, std::string, std::string, int, int)':
transcriptmapping.cpp:605:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(of, header);
                              ^
transcriptmapping.cpp: At global scope:
transcriptmapping.cpp:569:10: warning: 'void {anonymous}::report_every_3_mins(std::atomic<long long unsigned int>&, std::atomic<bool>&)' defined but not used [-Wunused-function]
     void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     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:92:27: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(fp, hdr);
                           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'int hamming_distance(std::string, std::string)':
utils.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < A.length(); ++i)
                       ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scPipe.dll tmp.def Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o transcriptmapping.o trimbarcode.o utils.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.buildbin-libdir/scPipe/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scPipe'
    finding HTML links ... done
    QC_metrics                              html  
    finding level-2 HTML links ... done

    UMI_dup_info                            html  
    UMI_duplication                         html  
    calculate_QC_metrics                    html  
    cell_barcode_matching                   html  
    convert_geneid                          html  
    create_processed_report                 html  
    create_report                           html  
    create_sce_by_dir                       html  
    demultiplex_info                        html  
    detect_outlier                          html  
    gene_id_type                            html  
    get_genes_by_GO                         html  
    organism                                html  
    plot_QC_pairs                           html  
    plot_UMI_dup                            html  
    plot_demultiplex                        html  
    plot_mapping                            html  
    remove_outliers                         html  
    scPipe                                  html  
    sc_count_aligned_bam                    html  
    sc_demultiplex                          html  
    sc_demultiplex_and_count                html  
    sc_detect_bc                            html  
    sc_exon_mapping                         html  
    sc_gene_counting                        html  
    sc_sample_data                          html  
    sc_sample_qc                            html  
    sc_trim_barcode                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scPipe' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Gene.cpp -o Gene.o
Gene.cpp: In member function 'void Gene::flatten_exon()':
Gene.cpp:103:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 1; i < exon_vec.size(); i++)
                        ^
Gene.cpp: In function 'std::ostream& operator<<(std::ostream&, const Gene&)':
Gene.cpp:128:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < obj.exon_vec.size(); ++i)
                       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Interval.cpp -o Interval.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cellbarcode.cpp -o cellbarcode.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c detect_barcode.cpp -o detect_barcode.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c parsebam.cpp -o parsebam.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c parsecount.cpp -o parsecount.o
parsecount.cpp: In function 'void write_stat(std::string, std::string, std::vector<int>, std::unordered_map<std::basic_string<char>, UMI_dedup_stat>)':
parsecount.cpp:134:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<UMI_dup_count.size(); i++)
                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:7:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.st < start)
                     ^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.en > end)
                     ^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         return !(start > it.en) && !(end < it.st);
                        ^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         return !(start > it.en) && !(end < it.st);
                                          ^
In file included from config_hts.h:8:0,
                 from trimbarcode.h:6,
                 from rcpp_scPipe_func.cpp:3:
trimbarcode.h: At global scope:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:170:16: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function]
  SCOPE kseq_t *kseq_init(type_t fd)         \
                ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:176:13: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function]
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:190:12: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  SCOPE int kseq_read(kseq_t *seq) \
            ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
  __KSEQ_READ(SCOPE)
  ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
trimbarcode.h:11:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c transcriptmapping.cpp -o transcriptmapping.o
In file included from transcriptmapping.cpp:2:0:
transcriptmapping.h: In member function 'void GeneBin::add_gene(Gene)':
transcriptmapping.h:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.st < start)
                     ^
transcriptmapping.h:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (gene.en > end)
                     ^
transcriptmapping.h: In member function 'const bool GeneBin::overlaps(const Interval&)':
transcriptmapping.h:53:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         return !(start > it.en) && !(end < it.st);
                        ^
transcriptmapping.h:53:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         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:464:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int c=0; c<b->core.n_cigar; c++)
                    ^
transcriptmapping.cpp: In member function 'void Mapping::parse_align(std::string, std::string, bool, std::string, std::string, std::string, std::string, int, int)':
transcriptmapping.cpp:605:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(of, header);
                              ^
transcriptmapping.cpp: At global scope:
transcriptmapping.cpp:569:10: warning: 'void {anonymous}::report_every_3_mins(std::atomic<long long unsigned int>&, std::atomic<bool>&)' defined but not used [-Wunused-function]
     void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     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:92:27: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(fp, hdr);
                           ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'int hamming_distance(std::string, std::string)':
utils.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < A.length(); ++i)
                       ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scPipe.dll tmp.def Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o transcriptmapping.o trimbarcode.o utils.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scPipe.buildbin-libdir/scPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scPipe' as scPipe_1.2.1.zip
* DONE (scPipe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'scPipe' successfully unpacked and MD5 sums checked
In R CMD INSTALL