Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 295/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
celda 1.22.0 (landing page) Joshua Campbell
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | 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 | ||||||||||
To the developers/maintainers of the celda package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/celda.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: celda |
Version: 1.22.0 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL celda |
StartedAt: 2024-11-19 21:25:04 -0000 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 21:26:57 -0000 (Tue, 19 Nov 2024) |
EllapsedTime: 112.9 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL celda ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘celda’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c DecontX.cpp -o DecontX.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25, from DecontX.cpp:1: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ DecontX.cpp: In function 'Eigen::SparseMatrix<double, 0, int> calculateNativeMatrix(const Eigen::MappedSparseMatrix<double>&, const Rcpp::NumericVector&, const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::IntegerVector&, const double&)': DecontX.cpp:321:10: warning: variable 'x' set but not used [-Wunused-but-set-variable] 321 | double x; | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c eigenMatMultInt.cpp -o eigenMatMultInt.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25, from eigenMatMultInt.cpp:3: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c matrixNorm.cpp -o matrixNorm.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c matrixSums.c -o matrixSums.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c matrixSumsSparse.cpp -o matrixSumsSparse.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25, from matrixSumsSparse.cpp:1: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]': /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper<int, 2>'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c perplexity.c -o perplexity.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o celda.so DecontX.o RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o matrixSumsSparse.o perplexity.o -fopenmp -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-celda/00new/celda/libs ** R ** data *** moving datasets to lazyload DB ** 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 (celda)