Back to Multiple platform build/check report for BioC 3.20: simplified long |
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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 557/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
destiny 3.20.0 (landing page) Philipp Angerer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | 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 | WARNINGS | ||||||||||
To the developers/maintainers of the destiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/destiny.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: destiny |
Version: 3.20.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings destiny_3.20.0.tar.gz |
StartedAt: 2024-11-20 07:09:46 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 07:15:15 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 328.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: destiny.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings destiny_3.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/destiny.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘destiny/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘destiny’ version ‘3.20.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .lintr .vscode These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘destiny’ can be installed ... WARNING Found the following significant warnings: /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] /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] See ‘/home/biocbuild/bbs-3.20-bioc/meat/destiny.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘rgl’ ‘SingleCellExperiment’ A package should be listed in only one of these fields. 'LinkingTo' for ‘grDevices’ is unused as it has no 'include' directory * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) Gene-Relevance.Rd:94: Escaped LaTeX specials: \_ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'coercions.Rd': ‘fortify.DiffusionMap’ ‘fortify.DPT’ S3 methods shown with full name in Rd file 'plot.DPT.Rd': ‘plot.DPT’ S3 methods shown with full name in Rd file 'plot.DiffusionMap.Rd': ‘plot.DiffusionMap’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Gene-Relevance-plotting 7.214 0.040 7.177 destiny 5.454 0.024 5.489 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/destiny.Rcheck/00check.log’ for details.
destiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL destiny ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘destiny’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -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'/home/biocbuild/R/R-4.4.1/library/grDevices/include' -I/usr/local/include -ggdb -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++11 -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'/home/biocbuild/R/R-4.4.1/library/grDevices/include' -I/usr/local/include -ggdb -fPIC -g -O2 -Wall -c censoring.cpp -o censoring.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 censoring.cpp:7: /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++11 -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'/home/biocbuild/R/R-4.4.1/library/grDevices/include' -I/usr/local/include -ggdb -fPIC -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o utils.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-destiny/00new/destiny/libs ** R ** data ** demo ** 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 (destiny)
destiny.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(destiny) > > test_check('destiny') [ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • Not yet stable (1): 'test_gr.r:23:2' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ] > > proc.time() user system elapsed 16.690 0.569 17.193
destiny.Rcheck/destiny-Ex.timings
name | user | system | elapsed | |
DPT-matrix-methods | 1.947 | 0.020 | 1.971 | |
DPT-methods | 2.439 | 0.040 | 2.482 | |
DPT | 1.043 | 0.016 | 1.061 | |
DiffusionMap-accessors | 0.500 | 0.016 | 0.516 | |
DiffusionMap-class | 4.269 | 0.064 | 4.337 | |
DiffusionMap-methods | 0.428 | 0.003 | 0.432 | |
ExpressionSet-helpers | 0.11 | 0.00 | 0.11 | |
Gene-Relevance-methods | 1.805 | 0.000 | 1.808 | |
Gene-Relevance-plotting | 7.214 | 0.040 | 7.177 | |
Gene-Relevance | 3.296 | 0.024 | 3.238 | |
Sigmas-class | 0.178 | 0.012 | 0.191 | |
coercions | 0.490 | 0.008 | 0.500 | |
colorlegend | 0.011 | 0.008 | 0.018 | |
cube_helix | 0.009 | 0.000 | 0.009 | |
destiny-generics | 0.546 | 0.020 | 0.566 | |
destiny | 5.454 | 0.024 | 5.489 | |
dm_predict | 1.405 | 0.060 | 1.467 | |
eig_decomp | 0.002 | 0.000 | 0.001 | |
extractions | 0.954 | 0.008 | 0.964 | |
find_dm_k | 0.008 | 0.003 | 0.012 | |
find_sigmas | 0.599 | 0.004 | 0.604 | |
find_tips | 0.508 | 0.004 | 0.513 | |
l_which | 0 | 0 | 0 | |
plot.DPT | 2.272 | 0.020 | 2.297 | |
plot.DiffusionMap | 0.725 | 0.036 | 0.763 | |
plot.Sigmas | 0.175 | 0.000 | 0.175 | |
projection_dist | 0.243 | 0.000 | 0.244 | |
random_root | 0.479 | 0.000 | 0.479 | |