Wenjie Sun
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/CellBarcode |
| git_branch: RELEASE_3_19 |
| git_last_commit: c3282ec |
| git_last_commit_date: 2024-04-30 11:38:56 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:39 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 296/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellBarcode 1.10.0 (landing page) Wenjie Sun
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the CellBarcode package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellBarcode.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: CellBarcode |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CellBarcode |
| StartedAt: 2024-05-08 20:34:40 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 20:36:20 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 100.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CellBarcode
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘CellBarcode’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c lib_10X_barcode.cpp -o lib_10X_barcode.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string.hpp:19,
from lib_10X_barcode.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/function/detail/prologue.hpp:19,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string.hpp:23,
from lib_10X_barcode.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/classification.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/trim.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string.hpp:19,
from lib_10X_barcode.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
lib_10X_barcode.cpp: In function ‘Rcpp::List parse_10x_sam(std::string, std::string, std::string, std::string)’:
lib_10X_barcode.cpp:84:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
84 | for (int j=11; j<parts.size(); j++) {
| ~^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c lib_clustering.cpp -o lib_clustering.o
lib_clustering.cpp: In function ‘int hamm_dist(std::string, std::string)’:
lib_clustering.cpp:59:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
59 | for (int i=0; i < s1.length(); i++) {
| ~~^~~~~~~~~~~~~
lib_clustering.cpp: In function ‘Rcpp::List seq_correct(std::vector<std::__cxx11::basic_string<char> >, Rcpp::IntegerVector, int, int, double, int, int, int, int)’:
lib_clustering.cpp:127:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
127 | for (auto i=0; i<seq.size(); i++) {
| ~^~~~~~~~~~~
lib_clustering.cpp:232:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
232 | for (auto i=0; i<res.size(); i++) {
| ~^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c lib_read_seq.cpp -o lib_read_seq.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o CellBarcode.so RcppExports.o lib_10X_barcode.o lib_clustering.o lib_read_seq.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-CellBarcode/00new/CellBarcode/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 (CellBarcode)