| Back to Multiple platform build/check report for BioC 3.18: simplified long | |
This page was generated on 2024-04-17 11:37:17 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake"
| 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
| 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake"
| 4437 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
| scPipe 2.2.0 (landing page)
Shian Su
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/scPipe |
| git_branch: RELEASE_3_18 |
| git_last_commit: 64848af |
| git_last_commit_date: 2023-10-24 11:00:35 -0400 (Tue, 24 Oct 2023) |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |  | |
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | |
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | |
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | |
BUILD BIN results for scPipe on palomino4
To the developers/maintainers of the scPipe package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scPipe.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
|
raw results
Summary
Command output
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###
### Running command:
###
### rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=scPipe.buildbin-libdir scPipe_2.2.0.tar.gz
###
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* installing *source* package 'scPipe' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentThread.cpp -o FragmentThread.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentUtils.cpp -o FragmentUtils.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ResizeArray.cpp -o ResizeArray.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadOutputFile.cpp -o ThreadOutputFile.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trie.cpp -o Trie.o
Trie.cpp: In member function 'void Trie::SeqMismatchAux(std::vector<MismatchResult>&, const std::string&, trie_node*, int, int, int) const':
Trie.cpp:265:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<trie_node*>::size_type' {aka 'long 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<trie_node*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
274 | for (int i = 0; i < valid_nodes.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cellbarcode.cpp -o cellbarcode.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_barcode_reads.cpp -o check_barcode_reads.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parsecount.cpp -o parsecount.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-cpp.cpp -o test-cpp.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-example.cpp -o test-example.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-fragmentThread.cpp -o test-fragmentThread.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-resizearray.cpp -o test-resizearray.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-str_utils.cpp -o test-str_utils.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-trie_matching.cpp -o test-trie_matching.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transcriptmapping.cpp -o transcriptmapping.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:612:24: warning: 'o_stream_gz' may be used uninitialized [-Wmaybe-uninitialized]
612 | fq_gz_write(o_stream_gz, seq1, bc1_end); // write to gzipped fastq file
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
trimbarcode.cpp:457:12: note: 'o_stream_gz' was declared here
457 | gzFile o_stream_gz;
| ^~~~~~~~~~~
trimbarcode.cpp: In function 'std::vector<int> 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:1163:9: warning: 'bc1_end' may be used uninitialized [-Wmaybe-uninitialized]
1163 | int bc1_end, bc2_end; // get end position in the read of barcode and umi
| ^~~~~~~
trimbarcode.cpp:1250:26: warning: 'seq3' may be used uninitialized [-Wmaybe-uninitialized]
1250 | if(find_N(seq3, id2_st, id2_len)){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
trimbarcode.cpp:1117:13: note: 'seq3' was declared here
1117 | kseq_t *seq3;
| ^~~~
trimbarcode.cpp:1499:16: warning: 'fq3' may be used uninitialized [-Wmaybe-uninitialized]
1499 | gzclose(fq3);
trimbarcode.cpp:1109:12: note: 'fq3' was declared here
1109 | gzFile fq3;
| ^~~
trimbarcode.cpp: In function 'std::vector<int> sc_atac_paired_fastq_to_fastq(const char*, std::vector<std::__cxx11::basic_string<char> >, const char*, const char*, const char*, bool, bool, bool, int, int, bool)':
trimbarcode.cpp:813:31: warning: 'seq3' may be used uninitialized [-Wmaybe-uninitialized]
813 | if((l3 = kseq_read(seq3)) < 0){
| ~~~~~~~~~^~~~~~
trimbarcode.cpp:750:13: note: 'seq3' was declared here
750 | kseq_t *seq3;
| ^~~~
trimbarcode.cpp:982:16: warning: 'fq3' may be used uninitialized [-Wmaybe-uninitialized]
982 | gzclose(fq3);
trimbarcode.cpp:721:16: note: 'fq3' was declared here
721 | gzFile fq3;
| ^~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsscreatebins.cpp -o tsscreatebins.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/testthat/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
g++ -shared -s -static-libgcc -o scPipe.dll tmp.def 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 F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/meat/scPipe.buildbin-libdir/00LOCK-scPipe/00new/scPipe/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'scPipe' as scPipe_2.2.0.zip
* DONE (scPipe)