##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scPipe.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scPipe_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scPipe.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scPipe' version '1.17.1'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'scPipe' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
* 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
Namespace in Imports field not imported from: 'scater'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
anno_to_saf: no visible binding for global variable 'GeneID'
convert_geneid: no visible global function definition for 'useMart'
get_genes_by_GO: no visible global function definition for 'useMart'
infer_gene_id_from_parent: no visible binding for global variable
  'type'
plot_demultiplex: no visible binding for global variable 'status'
plot_demultiplex: no visible binding for global variable 'count'
plot_demultiplex: no visible binding for global variable 'label_y'
plot_demultiplex: no visible binding for global variable 'label_tx'
Undefined global functions or variables:
  GeneID count label_tx label_y status type useMart
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/scPipe/libs/x64/scPipe.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plot_QC_pairs 5.78   0.03    5.82
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 6 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/scPipe.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scPipe
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'scPipe' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<Interval>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i = 0; i < obj.exon_vec.size(); ++i)
                     ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Interval.cpp -o Interval.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cellbarcode.cpp -o cellbarcode.o
cellbarcode.cpp: In member function 'std::__cxx11::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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
     for (int i = 0; i < hamming_dists.size(); i++)
                     ~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c detect_barcode.cpp -o detect_barcode.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c parsebam.cpp -o parsebam.o
parsebam.cpp: In member function 'int Bamdemultiplex::clean_bam_barcode(std::__cxx11::string, std::__cxx11::string, int, int)':
parsebam.cpp:78:9: warning: variable 'hts_retcode' set but not used [-Wunused-but-set-variable]
     int hts_retcode;
         ^~~~~~~~~~~
parsebam.cpp:116:9: warning: unused variable 'map_status' [-Wunused-variable]
     int map_status;
         ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c parsecount.cpp -o parsecount.o
parsecount.cpp: In function 'void write_stat(std::__cxx11::string, std::__cxx11::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 long unsigned int'} [-Wsign-compare]
     for (int i=0; i<UMI_dup_count.size(); i++)
                   ~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
         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]
         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]
         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]
         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:
D:/biocbuild/bbs-3.15-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) \
            ^~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: note: in definition of macro '__KSEQ_READ'
  SCOPE int kseq_read(kseq_t *seq) \
            ^~~~~~~~~
D:/biocbuild/bbs-3.15-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)
 ^~~~~~~~~
D:/biocbuild/bbs-3.15-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)         \
             ^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: note: in definition of macro '__KSEQ_BASIC'
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-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)
 ^~~~~~~~~
D:/biocbuild/bbs-3.15-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)         \
                ^~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: in definition of macro '__KSEQ_BASIC'
  SCOPE kseq_t *kseq_init(type_t fd)         \
                ^~~~~~~~~
D:/biocbuild/bbs-3.15-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:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c test-cpp.cpp -o test-cpp.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c test-runner.cpp -o test-runner.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include/testthat.h:1,
                 from test-runner.cpp:7:
D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include/testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
         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]
         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]
         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]
         return !(start > it.en) && !(end < it.st);
                                      ~~~~^~~~~~~
transcriptmapping.cpp: In member function 'int Mapping::map_exon(bam_hdr_t*, bam1_t*, std::__cxx11::string&, bool)':
transcriptmapping.cpp:533:20: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-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::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, bool, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::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 long unsigned int'} [-Wsign-compare]
       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 long unsigned int'} [-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::__cxx11::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::__cxx11::string, std::__cxx11::string, bool, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, std::__cxx11::string, int, int)':
transcriptmapping.cpp:755:9: warning: variable 'hts_retcode' set but not used [-Wunused-but-set-variable]
     int hts_retcode;
         ^~~~~~~~~~~
transcriptmapping.cpp: At global scope:
transcriptmapping.cpp:699:25: warning: 'std::pair<int, int> {anonymous}::get_bc_umi_lengths(std::__cxx11::string)' defined but not used [-Wunused-function]
     std::pair<int, int> get_bc_umi_lengths(string bam_fn) {
                         ^~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
     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]
     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]
             fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
             ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/testthat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c utils.cpp -o utils.o
C:/rtools40/mingw64/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 D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-scPipe/00new/scPipe/libs/x64
** 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  
    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_correct_bam_bc                       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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scPipe)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'plotgardener' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scPipe)
Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians



> 
> test_check("scPipe")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
  11.17    0.93   12.12