############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL scPipe ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘scPipe’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c FragmentThread.cpp -o FragmentThread.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c FragmentUtils.cpp -o FragmentUtils.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Gene.cpp -o Gene.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c ResizeArray.cpp -o ResizeArray.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c ThreadOutputFile.cpp -o ThreadOutputFile.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c Trie.cpp -o Trie.o Trie.cpp: In member function ‘void Trie::SeqMismatchAux(std::vector&, const string&, trie_node*, int, int, int) const’: Trie.cpp:265:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 265 | for (int i = 0; i < valid_nodes.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ Trie.cpp:274:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 274 | for (int i = 0; i < valid_nodes.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam.c -o bam.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c cellbarcode.cpp -o cellbarcode.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c check_barcode_reads.cpp -o check_barcode_reads.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c parsecount.cpp -o parsecount.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-example.cpp -o test-example.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-fragmentThread.cpp -o test-fragmentThread.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-resizearray.cpp -o test-resizearray.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-str_utils.cpp -o test-str_utils.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-trie_matching.cpp -o test-trie_matching.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c transcriptmapping.cpp -o transcriptmapping.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c trimbarcode.cpp -o trimbarcode.o trimbarcode.cpp: In function ‘void paired_fastq_to_fastq(char*, char*, char*, read_s, filter_s, bool)’: trimbarcode.cpp:611:24: warning: ‘o_stream_gz’ may be used uninitialized in this function [-Wmaybe-uninitialized] 611 | fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ trimbarcode.cpp: In function ‘std::vector sc_atac_paired_fastq_to_csv(char*, char*, char*, char*, char*, int, int, char*, bool, bool, bool, int, int, int, int, int, int)’: trimbarcode.cpp:1347:68: warning: ‘bc1_end’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1347 | memmove(seq1->seq.s, seq1->seq.s + bc1_end, seq1->name.l - bc1_end); | ^~~~~~~ trimbarcode.cpp:1406:57: warning: ‘seq3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1406 | memcpy(subStr3 + id2_len + 1, seq3->seq.s + umi_start, umi_length); | ~~~~~~~~~~^ trimbarcode.cpp:1498:16: warning: ‘fq3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1498 | gzclose(fq3); | ~~~~~~~^~~~~ trimbarcode.cpp: In function ‘std::vector sc_atac_paired_fastq_to_fastq(const char*, std::vector >, const char*, const char*, const char*, bool, bool, bool, int, int, bool)’: trimbarcode.cpp:812:31: warning: ‘seq3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 812 | if((l3 = kseq_read(seq3)) < 0){ | ~~~~~~~~~^~~~~~ trimbarcode.cpp:981:16: warning: ‘fq3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 981 | gzclose(fq3); | ~~~~~~~^~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c tsscreatebins.cpp -o tsscreatebins.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o scPipe.so FragmentThread.o FragmentUtils.o Gene.o Interval.o RcppExports.o ResizeArray.o ThreadOutputFile.o Trie.o bam.o cellbarcode.o check_barcode_reads.o detect_barcode.o parsebam.o parsecount.o qc_per_bc_file_helper.o rcpp_scPipe_func.o sc_atac_create_fragments.o test-cpp.o test-example.o test-fragmentThread.o test-resizearray.o test-runner.o test-str_utils.o test-trie_matching.o transcriptmapping.o trimbarcode.o tsscreatebins.o utils.o /home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)