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INSTALL report for scPipe on malbec2

This page was generated on 2019-10-16 12:12:24 -0400 (Wed, 16 Oct 2019).

Package 1476/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPipe 1.6.0
Luyi Tian
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/scPipe
Branch: RELEASE_3_9
Last Commit: 804095b
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scPipe
Version: 1.6.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scPipe
StartedAt: 2019-10-15 18:55:54 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:57:43 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 108.6 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scPipe
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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, std::unordered_map, UMI_dedup_stat>)’:
parsecount.cpp:216:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i 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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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; ccore.n_cigar; c++)
                   ~^~~~~~~~~~~~~~~~
transcriptmapping.cpp: In member function ‘void Mapping::parse_align_warpper(std::vector >, std::vector >, 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 {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 {anonymous}::get_bc_umi_lengths(std::__cxx11::string)’ defined but not used [-Wunused-function]
     std::pair get_bc_umi_lengths(string bam_fn) {
                         ^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)