Jiaxing Lin
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/bcSeq |
| git_branch: RELEASE_3_19 |
| git_last_commit: 69bf97b |
| git_last_commit_date: 2024-04-30 11:02:42 -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 11:40:35 -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 144/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bcSeq 1.26.0 (landing page) Jiaxing Lin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the bcSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bcSeq.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: bcSeq |
| Version: 1.26.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL bcSeq |
| StartedAt: 2024-05-08 20:11:23 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 20:12:42 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 78.8 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 bcSeq
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘bcSeq’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c CRISPR_matching.cpp -o CRISPR_matching.o
In file included from helper/../structures/Trie.h:16,
from helper/count.h:5,
from CRISPR_matching.cpp:3:
helper/../structures/NodePool.h: In member function ‘void Pool::resize()’:
helper/../structures/NodePool.h:58:52: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct Node’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
58 | std::memcpy(x, buff.get(), count * sizeof(Node));
| ^
In file included from helper/../structures/Trie.h:15,
from helper/count.h:5,
from CRISPR_matching.cpp:3:
helper/../structures/Node.h:11:8: note: ‘struct Node’ declared here
11 | struct Node {
| ^~~~
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c Trie_edit.cpp -o Trie_edit.o
In file included from structures/Trie.h:16,
from Trie_edit.cpp:1:
structures/NodePool.h: In member function ‘void Pool::resize()’:
structures/NodePool.h:58:52: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct Node’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
58 | std::memcpy(x, buff.get(), count * sizeof(Node));
| ^
In file included from structures/Trie.h:15,
from Trie_edit.cpp:1:
structures/Node.h:11:8: note: ‘struct Node’ declared here
11 | struct Node {
| ^~~~
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c Trie_hamming.cpp -o Trie_hamming.o
In file included from structures/Trie.h:16,
from Trie_hamming.cpp:1:
structures/NodePool.h: In member function ‘void Pool::resize()’:
structures/NodePool.h:58:52: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct Node’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
58 | std::memcpy(x, buff.get(), count * sizeof(Node));
| ^
In file included from structures/Trie.h:15,
from Trie_hamming.cpp:1:
structures/Node.h:11:8: note: ‘struct Node’ declared here
11 | struct Node {
| ^~~~
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c Trie_util.cpp -o Trie_util.o
In file included from structures/Trie.h:16,
from Trie_util.cpp:2:
structures/NodePool.h: In member function ‘void Pool::resize()’:
structures/NodePool.h:58:52: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct Node’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
58 | std::memcpy(x, buff.get(), count * sizeof(Node));
| ^
In file included from structures/Trie.h:15,
from Trie_util.cpp:2:
structures/Node.h:11:8: note: ‘struct Node’ declared here
11 | struct Node {
| ^~~~
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c alignment.cpp -o alignment.o
gcc -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/library/Matrix/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c trimRead.cpp -o trimRead.o
g++ -std=gnu++11 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -c uniqueBar.cpp -o uniqueBar.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.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-bcSeq/00new/bcSeq/libs
** R
** 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 (bcSeq)