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CHECK report for scPipe on tokay1

This page was generated on 2020-04-15 12:29:17 -0400 (Wed, 15 Apr 2020).

Package 1544/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPipe 1.8.0
Luyi Tian
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/scPipe
Branch: RELEASE_3_10
Last Commit: 8b19bf1
Last Changed Date: 2019-10-29 13:10:51 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scPipe
Version: 1.8.0
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scPipe_1.8.0.tar.gz
StartedAt: 2020-04-15 06:28:28 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:35:16 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 407.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: scPipe.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scPipe_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/scPipe.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.8.0'
* 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 whether package 'scPipe' can be installed ... WARNING
Found the following significant warnings:
  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]
  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]
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/scPipe.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/scPipe/libs/i386/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)
File 'C:/Users/biocbuild/bbs-3.10-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 ...
** running examples for arch 'i386' ... 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  8.36   0.13    8.48
sc_sample_data 5.44   0.01    5.45
convert_geneid 0.67   0.06    8.61
** running examples for arch 'x64' ... 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        10.66   0.01   10.67
sc_sample_data        9.91   0.00    9.91
calculate_QC_metrics  2.33   0.16    6.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/scPipe.Rcheck/00check.log'
for details.



Installation output

scPipe.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/scPipe_1.8.0.tar.gz && rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scPipe.buildbin-libdir scPipe_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL scPipe_1.8.0.zip && rm scPipe_1.8.0.tar.gz scPipe_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  955k  100  955k    0     0  5397k      0 --:--:-- --:--:-- --:--:-- 5522k

install for i386

* installing *source* package 'scPipe' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Interval.cpp -o Interval.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c detect_barcode.cpp -o detect_barcode.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c parsebam.cpp -o parsebam.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-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-3.10-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-3.10-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)
 ^
C:/Users/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)         \
             ^
C:/Users/biocbuild/bbs-3.10-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-3.10-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)
 ^
C:/Users/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) \
            ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
  __KSEQ_READ(SCOPE)
  ^
C:/Users/biocbuild/bbs-3.10-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)
 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c test-cpp.cpp -o test-cpp.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat.h:1:0,
                 from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h:140:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h:147:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/scPipe.buildbin-libdir/00LOCK-scPipe/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'scPipe' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Interval.cpp -o Interval.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c detect_barcode.cpp -o detect_barcode.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c parsebam.cpp -o parsebam.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-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-3.10-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-3.10-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)
 ^
C:/Users/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)         \
             ^
C:/Users/biocbuild/bbs-3.10-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-3.10-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)
 ^
C:/Users/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) \
            ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/kseq.h:242:2: note: in expansion of macro '__KSEQ_READ'
  __KSEQ_READ(SCOPE)
  ^
C:/Users/biocbuild/bbs-3.10-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)
 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c test-cpp.cpp -o test-cpp.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat.h:1:0,
                 from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h:140:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h:147:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/scPipe.buildbin-libdir/scPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scPipe' as scPipe_1.8.0.zip
* DONE (scPipe)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'scPipe' successfully unpacked and MD5 sums checked

Tests output

scPipe.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 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

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")'.

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 
  15.18    1.20   16.43 

scPipe.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 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

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")'.

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 
  16.75    0.59   17.39 

Example timings

scPipe.Rcheck/examples_i386/scPipe-Ex.timings

nameusersystemelapsed
QC_metrics0.250.020.26
UMI_dup_info0.110.060.18
UMI_duplication0.060.100.16
anno_import2.330.202.54
anno_to_saf0.260.000.27
calculate_QC_metrics1.270.064.95
cell_barcode_matching0.110.050.16
convert_geneid0.670.068.61
create_processed_report000
create_report000
create_sce_by_dir0.090.000.10
demultiplex_info0.080.010.10
detect_outlier0.310.040.34
gene_id_type0.140.000.14
get_ercc_anno0.590.010.93
get_genes_by_GO0.830.032.79
get_read_str000
organism0.110.000.11
plot_QC_pairs8.360.138.48
plot_UMI_dup0.310.030.34
plot_demultiplex0.230.010.25
plot_mapping0.610.040.64
remove_outliers0.250.030.29
sc_count_aligned_bam000
sc_demultiplex000
sc_demultiplex_and_count000
sc_detect_bc000
sc_exon_mapping000
sc_gene_counting000
sc_sample_data5.440.015.45
sc_sample_qc0.670.000.68
sc_trim_barcode000

scPipe.Rcheck/examples_x64/scPipe-Ex.timings

nameusersystemelapsed
QC_metrics0.330.000.33
UMI_dup_info0.830.020.85
UMI_duplication0.120.010.14
anno_import2.060.082.14
anno_to_saf1.080.001.08
calculate_QC_metrics2.330.166.00
cell_barcode_matching0.190.010.20
convert_geneid1.220.032.84
create_processed_report000
create_report0.010.000.02
create_sce_by_dir0.20.00.2
demultiplex_info0.180.020.19
detect_outlier0.430.020.45
gene_id_type0.160.010.18
get_ercc_anno0.760.020.85
get_genes_by_GO0.940.042.60
get_read_str000
organism0.170.040.21
plot_QC_pairs10.66 0.0110.67
plot_UMI_dup0.580.020.59
plot_demultiplex0.530.000.53
plot_mapping1.180.001.27
remove_outliers0.360.010.38
sc_count_aligned_bam000
sc_demultiplex000
sc_demultiplex_and_count000
sc_detect_bc000
sc_exon_mapping000
sc_gene_counting000
sc_sample_data9.910.009.91
sc_sample_qc1.060.051.11
sc_trim_barcode000