Package: scPipe

Version: 1.8.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scPipe_1.8.0.tar.gz

StartedAt: 2020-04-15 05:13:59 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:18:50 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 290.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scPipe.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scPipe_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/scPipe.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  transcriptmapping.cpp:756:18: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
  trimbarcode.cpp:92:18: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.10-bioc/meat/scPipe.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
* 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 ... OK
* 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 ‘type’
anno_to_saf: no visible binding for global variable ‘gene_id’
anno_to_saf: no visible binding for global variable ‘seqnames’
anno_to_saf: no visible binding for global variable ‘start’
anno_to_saf: no visible binding for global variable ‘end’
anno_to_saf: no visible binding for global variable ‘strand’
anno_to_saf: no visible binding for global variable ‘GeneID’
infer_gene_id_from_parent : <local>: no visible binding for global
  variable ‘transcript_id’
infer_gene_id_from_parent : <local>: no visible binding for global
  variable ‘Parent’
infer_gene_id_from_parent: no visible binding for global variable
  ‘type’
infer_gene_id_from_parent: no visible binding for global variable
  ‘Parent’
infer_gene_id_from_parent: no visible binding for global variable
  ‘gene_id’
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 Parent count end gene_id label_tx label_y seqnames start
  status strand transcript_id type
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.10-bioc/R/library/scPipe/libs/scPipe.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
  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 ... WARNING
Found the following significant warnings:

  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                      user system elapsed
plot_QC_pairs        9.344  0.012   9.376
sc_sample_data       8.292  0.000   8.298
calculate_QC_metrics 2.452  0.044   9.744
convert_geneid       0.844  0.032  13.589
* 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: 2 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/scPipe.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scPipe
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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 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)
                     ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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::__cxx11::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++)
                     ~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/testthat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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::__cxx11::string, std::__cxx11::string, std::vector<int>, std::unordered_map<std::__cxx11::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++)
                   ~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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:7:0:
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:
/home/biocbuild/bbs-3.10-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) \
            ^
/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: note: in definition of macro ‘__KSEQ_READ’
  SCOPE int kseq_read(kseq_t *seq) \
            ^~~~~~~~~
/home/biocbuild/bbs-3.10-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)
 ^
/home/biocbuild/bbs-3.10-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)         \
             ^
/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: note: in definition of macro ‘__KSEQ_BASIC’
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.10-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)
 ^
/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
  SCOPE kseq_t *kseq_init(type_t fd)         \
                ^
/home/biocbuild/bbs-3.10-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)         \
                ^~~~~~~~~
/home/biocbuild/bbs-3.10-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)
 ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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:2:0:
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::__cxx11::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::__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 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::__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:756:18: 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::__cxx11::string)’ defined but not used [-Wunused-function]
     std::pair<int, int> get_bc_umi_lengths(string bam_fn) {
                         ^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-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 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:92:18: 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:449:24: 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
             ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/testthat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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)
                     ~~^~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-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-3.10-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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> library(testthat)
> library(scPipe)
Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum



> 
> test_check("scPipe")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 27 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 16.608   0.560  17.230 

name	user	system	elapsed
QC_metrics	0.404	0.000	0.405
UMI_dup_info	0.808	0.004	0.815
UMI_duplication	0.168	0.000	0.169
anno_import	3.560	0.024	3.623
anno_to_saf	0.336	0.008	0.341
calculate_QC_metrics	2.452	0.044	9.744
cell_barcode_matching	0.148	0.012	0.160
convert_geneid	0.844	0.032	13.589
create_processed_report	0	0	0
create_report	0	0	0
create_sce_by_dir	0.124	0.000	0.127
demultiplex_info	0.100	0.000	0.103
detect_outlier	0.256	0.004	0.261
gene_id_type	0.104	0.000	0.102
get_ercc_anno	0.572	0.000	0.665
get_genes_by_GO	0.680	0.012	2.634
get_read_str	0.000	0.000	0.001
organism	0.184	0.004	0.187
plot_QC_pairs	9.344	0.012	9.376
plot_UMI_dup	0.508	0.000	0.507
plot_demultiplex	0.432	0.000	0.430
plot_mapping	1.056	0.012	1.071
remove_outliers	0.472	0.000	0.473
sc_count_aligned_bam	0	0	0
sc_demultiplex	0.004	0.000	0.001
sc_demultiplex_and_count	0	0	0
sc_detect_bc	0	0	0
sc_exon_mapping	0.004	0.000	0.001
sc_gene_counting	0.000	0.000	0.001
sc_sample_data	8.292	0.000	8.298
sc_sample_qc	0.692	0.008	0.701
sc_trim_barcode	0	0	0