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 1263/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.14.0 (landing page) Rui Guan
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the mina package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mina.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: mina |
Version: 1.14.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mina_1.14.0.tar.gz |
StartedAt: 2024-11-20 09:53:40 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 09:59:14 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 333.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mina_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mina.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 ‘mina/DESCRIPTION’ ... OK * this is package ‘mina’ version ‘1.14.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mina’ can be installed ... OK * used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... NOTE installed size is 9.1Mb sub-directories of 1Mb or more: data 7.4Mb libs 1.2Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 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 ... NOTE sparcc: no visible binding for global variable ‘i’ net_dis_pcoa,character: no visible binding for global variable ‘y’ net_dis_pcoa,character: no visible binding for global variable ‘Group’ net_dis_plot,mina: no visible binding for global variable ‘Group1’ net_dis_plot,mina: no visible binding for global variable ‘Group2’ net_dis_plot,mina: no visible binding for global variable ‘Distance’ net_dis_plot,mina: no visible binding for global variable ‘Sig’ Undefined global functions or variables: Distance Group Group1 Group2 Sig i y * checking Rd files ... NOTE checkRd: (-1) re_format_AP.Rd:10: Lost braces; missing escapes or markup? 10 | \item{x}{an {APResult} object from \pkg{apcluster}.} | ^ * 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 ... OK * 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 LazyData ... WARNING LazyData DB of 7.4 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... 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 net_dis_plot 91.095 1.693 87.099 net_dis-mina 46.413 0.675 44.377 dis_stat_accessor 33.128 0.938 31.945 com_plot-mina 22.960 0.043 3.299 net_cls-mina 12.398 0.040 10.056 bs_pm-mina 10.226 0.501 8.576 net_cls 5.113 0.036 2.815 net_cls-matrix 5.083 0.020 2.733 * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/mina.Rcheck/00check.log’ for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs 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/RcppParallel/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.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/RcppParallel/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cp_cor.cpp -o cp_cor.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24, from cp_cor.cpp:6: /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-mina/00new/mina/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘norm’ in package ‘mina’ ** 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 (mina)
mina.Rcheck/mina-Ex.timings
name | user | system | elapsed | |
adj-matrix | 1.080 | 0.030 | 0.473 | |
adj-mina | 1.580 | 0.011 | 0.919 | |
adj | 1.275 | 0.000 | 0.614 | |
adj_method_list | 0.082 | 0.008 | 0.098 | |
bs_pm-mina | 10.226 | 0.501 | 8.576 | |
bs_pm | 2.550 | 0.110 | 2.298 | |
check_mina | 0.112 | 0.008 | 0.120 | |
check_mina_de | 0.109 | 0.000 | 0.109 | |
check_mina_qu | 0.108 | 0.000 | 0.108 | |
cls_tab | 0.109 | 0.000 | 0.111 | |
com_dis-matrix | 0.744 | 0.011 | 0.417 | |
com_dis-mina | 0.441 | 0.004 | 0.138 | |
com_dis | 0.699 | 0.004 | 0.400 | |
com_dis_list | 0.105 | 0.014 | 0.118 | |
com_plot-mina | 22.960 | 0.043 | 3.299 | |
com_plot | 0.225 | 0.000 | 0.218 | |
com_r2-mina | 1.019 | 0.000 | 0.689 | |
com_r2 | 2.325 | 0.011 | 1.546 | |
data-hmp | 0.002 | 0.000 | 0.001 | |
data-maize | 0.001 | 0.000 | 0.000 | |
des_accessor | 0.003 | 0.000 | 0.003 | |
dis_accessor | 0.392 | 0.001 | 0.084 | |
dis_stat_accessor | 33.128 | 0.938 | 31.945 | |
dmr-matrix | 0.750 | 0.016 | 0.457 | |
dmr-mina | 0.846 | 0.016 | 0.451 | |
dmr | 0.870 | 0.005 | 0.442 | |
dmr_accessor | 0.851 | 0.036 | 0.478 | |
fit_tabs-mina | 1.862 | 0.024 | 1.805 | |
fit_tabs | 2.014 | 0.020 | 2.038 | |
get_net_cls_tab-matrix-data.frame-method | 2.606 | 0.012 | 1.986 | |
get_net_cls_tab | 2.642 | 0.020 | 2.037 | |
get_r2-mat | 0.946 | 0.007 | 0.619 | |
get_r2 | 0.969 | 0.005 | 0.689 | |
get_rep-matrix | 0.663 | 0.015 | 0.679 | |
get_rep-mima | 1.508 | 0.000 | 1.510 | |
hmp_des | 0.001 | 0.000 | 0.001 | |
hmp_otu | 0.001 | 0.000 | 0.001 | |
maize_asv | 0.001 | 0.000 | 0.001 | |
maize_asv2 | 0.001 | 0.000 | 0.001 | |
maize_des | 0.001 | 0.000 | 0.001 | |
maize_des2 | 0.000 | 0.000 | 0.001 | |
mina-class | 0.001 | 0.000 | 0.001 | |
net_cls-matrix | 5.083 | 0.020 | 2.733 | |
net_cls-mina | 12.398 | 0.040 | 10.056 | |
net_cls | 5.113 | 0.036 | 2.815 | |
net_cls_tab-mina-method | 4.040 | 0.011 | 2.094 | |
net_cls_tab | 2.684 | 0.004 | 2.051 | |
net_dis-mina | 46.413 | 0.675 | 44.377 | |
net_dis | 2.204 | 0.237 | 2.281 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
net_dis_plot | 91.095 | 1.693 | 87.099 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0.001 | 0.000 | 0.000 | |
norm_accessor | 0.056 | 0.000 | 0.056 | |
norm_tab-matrix | 1.134 | 0.032 | 1.168 | |
norm_tab-mina | 1.092 | 0.004 | 1.100 | |
norm_tab | 0.054 | 0.000 | 0.054 | |
norm_tab_method_list | 0.060 | 0.012 | 0.071 | |
pcoa_plot | 1.855 | 0.015 | 1.090 | |
sim_par | 0.001 | 0.000 | 0.000 | |
sparcc | 0.000 | 0.004 | 0.001 | |
tab_accessor | 0 | 0 | 0 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0 | 0 | 0 | |