scPipe 1.4.1
Luyi Tian
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/scPipe |
| Branch: RELEASE_3_8 |
| Last Commit: 90a617d |
| Last Changed Date: 2019-01-04 13:49:55 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/scPipe_1.4.1.tar.gz && rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scPipe.buildbin-libdir scPipe_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL scPipe_1.4.1.zip && rm scPipe_1.4.1.tar.gz scPipe_1.4.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1724k 100 1724k 0 0 19.4M 0 --:--:-- --:--:-- --:--:-- 20.2M
install for i386
* installing *source* package 'scPipe' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:105:24: 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:130:23: 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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < barcode_list.size(); i++)
^
cellbarcode.cpp:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < hamming_dists.size(); i++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:216:20: 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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:42:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:46:21: 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:54:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:54:42: 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-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
__KSEQ_READ(SCOPE)
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test-cpp.cpp -o test-cpp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:42:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:46:21: 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:54:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:54:42: 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:533:20: 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_warpper(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::string, bool, std::string, std::string, std::string, std::string, int, int, int)':
transcriptmapping.cpp:678:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1;i<fn_vec.size();i++)
^
transcriptmapping.cpp:686:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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:756:30: 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:699:25: warning: 'std::pair<int, int> {anonymous}::get_bc_umi_lengths(std::string)' defined but not used [-Wunused-function]
std::pair<int, int> get_bc_umi_lengths(string bam_fn) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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);
^
trimbarcode.cpp: In function 'void paired_fastq_to_fastq(char*, char*, char*, read_s, filter_s, bool)':
trimbarcode.cpp:449:52: warning: 'o_stream_gz' may be used uninitialized in this function [-Wmaybe-uninitialized]
fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'int hamming_distance(const string&, const string&)':
utils.cpp:24:23: 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 test-cpp.o test-runner.o transcriptmapping.o trimbarcode.o utils.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-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
anno_import html
anno_to_saf 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
dot-qq_outliers_robust html
gene_id_type html
get_ercc_anno html
get_genes_by_GO html
get_read_str 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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:105:24: 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:130:23: 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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < barcode_list.size(); i++)
^
cellbarcode.cpp:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < hamming_dists.size(); i++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:216:20: 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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:42:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:46:21: 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:54:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:54:42: 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-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/kseq.h:241:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/Rhtslib/include/htslib/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
__KSEQ_READ(SCOPE)
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include/htslib/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test-cpp.cpp -o test-cpp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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:42:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gene.st < start)
^
transcriptmapping.h:46:21: 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:54:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
return !(start > it.en) && !(end < it.st);
^
transcriptmapping.h:54:42: 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:533:20: 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_warpper(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::string, bool, std::string, std::string, std::string, std::string, int, int, int)':
transcriptmapping.cpp:678:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=1;i<fn_vec.size();i++)
^
transcriptmapping.cpp:686:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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:756:30: 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:699:25: warning: 'std::pair<int, int> {anonymous}::get_bc_umi_lengths(std::string)' defined but not used [-Wunused-function]
std::pair<int, int> get_bc_umi_lengths(string bam_fn) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/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);
^
trimbarcode.cpp: In function 'void paired_fastq_to_fastq(char*, char*, char*, read_s, filter_s, bool)':
trimbarcode.cpp:449:52: warning: 'o_stream_gz' may be used uninitialized in this function [-Wmaybe-uninitialized]
fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'int hamming_distance(const string&, const string&)':
utils.cpp:24:23: 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 test-cpp.o test-runner.o transcriptmapping.o trimbarcode.o utils.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/scPipe.buildbin-libdir/scPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scPipe' as scPipe_1.4.1.zip
* DONE (scPipe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'scPipe' successfully unpacked and MD5 sums checked
In R CMD INSTALL