Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -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 148/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bcSeq 1.29.0 (landing page) Jiaxing Lin
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.29.0 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL bcSeq |
StartedAt: 2024-12-23 19:33:54 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:34:46 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 51.5 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL bcSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘bcSeq’ ... ** 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 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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:58:16: 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: helper/../structures/Node.h:11:8: note: ‘struct Node’ declared here 11 | struct Node { | ^~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -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/library/Matrix/include' -I/usr/local/include -pthread -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 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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:58:16: 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: structures/Node.h:11:8: note: ‘struct Node’ declared here 11 | struct Node { | ^~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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:58:16: 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: structures/Node.h:11:8: note: ‘struct Node’ declared here 11 | struct Node { | ^~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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:58:16: 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: structures/Node.h:11:8: note: ‘struct Node’ declared here 11 | struct Node { | ^~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c alignment.cpp -o alignment.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -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/library/Matrix/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init.c -o init.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 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c trimRead.cpp -o trimRead.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 -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/library/Matrix/include' -I/usr/local/include -pthread -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c uniqueBar.cpp -o uniqueBar.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 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/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)