Shian Su
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/scPipe |
| git_branch: devel |
| git_last_commit: 53eacce |
| git_last_commit_date: 2024-12-17 00:09:20 -0500 (Tue, 17 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 | ||||
| Package 1881/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scPipe 2.7.1 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: scPipe |
| Version: 2.7.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL scPipe |
| StartedAt: 2024-12-23 20:13:58 -0000 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 20:17:15 -0000 (Mon, 23 Dec 2024) |
| EllapsedTime: 197.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL scPipe
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c FragmentThread.cpp -o FragmentThread.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c FragmentUtils.cpp -o FragmentUtils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Gene.cpp -o Gene.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Interval.cpp -o Interval.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c ResizeArray.cpp -o ResizeArray.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c ThreadOutputFile.cpp -o ThreadOutputFile.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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 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 unsigned int’} [-Wsign-compare]
274 | for (int i = 0; i < valid_nodes.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bam.c -o bam.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c cellbarcode.cpp -o cellbarcode.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c check_barcode_reads.cpp -o check_barcode_reads.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c detect_barcode.cpp -o detect_barcode.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c parsebam.cpp -o parsebam.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c parsecount.cpp -o parsecount.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c qc_per_bc_file_helper.cpp -o qc_per_bc_file_helper.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c sc_atac_create_fragments.cpp -o sc_atac_create_fragments.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-cpp.cpp -o test-cpp.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-example.cpp -o test-example.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-fragmentThread.cpp -o test-fragmentThread.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-resizearray.cpp -o test-resizearray.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-str_utils.cpp -o test-str_utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-trie_matching.cpp -o test-trie_matching.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c transcriptmapping.cpp -o transcriptmapping.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c trimbarcode.cpp -o trimbarcode.o
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:981:16: warning: ‘fq3’ may be used uninitialized [-Wmaybe-uninitialized]
981 | gzclose(fq3);
| ~~~~~~~^~~~~
trimbarcode.cpp:720:16: note: ‘fq3’ was declared here
720 | gzFile fq3;
| ^~~
trimbarcode.cpp:812:31: warning: ‘seq3’ may be used uninitialized [-Wmaybe-uninitialized]
812 | if((l3 = kseq_read(seq3)) < 0){
| ~~~~~~~~~^~~~~~
trimbarcode.cpp:749:13: note: ‘seq3’ was declared here
749 | kseq_t *seq3;
| ^~~~
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:1498:16: warning: ‘fq3’ may be used uninitialized [-Wmaybe-uninitialized]
1498 | gzclose(fq3);
| ~~~~~~~^~~~~
trimbarcode.cpp:1108:12: note: ‘fq3’ was declared here
1108 | gzFile fq3;
| ^~~
trimbarcode.cpp:1116:13: warning: ‘seq3’ may be used uninitialized [-Wmaybe-uninitialized]
1116 | kseq_t *seq3;
| ^~~~
trimbarcode.cpp:1203:9: warning: ‘bc1_end’ may be used uninitialized [-Wmaybe-uninitialized]
1203 | if (bc1_end > (int)seq1->seq.l) {
| ^~
trimbarcode.cpp:1162:9: note: ‘bc1_end’ was declared here
1162 | int bc1_end, bc2_end; // get end position in the read of barcode and umi
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c tsscreatebins.cpp -o tsscreatebins.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/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/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-scPipe/00new/scPipe/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (scPipe)