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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scPipe_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/scPipe.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scPipe’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scPipe’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
* 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 is not available
File ‘/home/biocbuild/bbs-3.13-bioc/R/library/scPipe/libs/scPipe.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 4.999   0.06   5.059
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/scPipe.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL scPipe
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)

R version 4.1.1 (2021-08-10) -- "Kick Things"
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> 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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
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 3 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 15.075   0.817  15.886