Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 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" | 4372 |
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 1256/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.15.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | 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 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: 1.15.0 |
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_1.15.0.tar.gz |
StartedAt: 2024-12-23 09:36:51 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 09:42:17 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 326.4 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_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mina.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mina/DESCRIPTION’ ... OK * this is package ‘mina’ version ‘1.15.0’ * 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking installed package size ... INFO 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 89.256 1.214 85.707 net_dis-mina 44.738 0.690 43.093 dis_stat_accessor 32.152 0.628 31.181 com_plot-mina 24.620 0.077 3.560 net_cls-mina 12.025 0.047 11.488 bs_pm-mina 10.203 0.654 9.200 * 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-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-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -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/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I/usr/local/include -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++17 -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/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c cp_cor.cpp -o cp_cor.o In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/tbb/tbb.h:32, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/RcppParallel/TBB.h:10, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/RcppParallel.h:24, from cp_cor.cpp:6: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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; | ^~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 | 1.050 | 0.046 | 0.475 | |
adj-mina | 1.514 | 0.007 | 0.939 | |
adj | 1.271 | 0.008 | 0.682 | |
adj_method_list | 0.064 | 0.015 | 0.092 | |
bs_pm-mina | 10.203 | 0.654 | 9.200 | |
bs_pm | 2.162 | 0.212 | 2.206 | |
check_mina | 0.108 | 0.040 | 0.149 | |
check_mina_de | 0.126 | 0.016 | 0.143 | |
check_mina_qu | 0.114 | 0.028 | 0.142 | |
cls_tab | 0.127 | 0.012 | 0.140 | |
com_dis-matrix | 0.625 | 0.024 | 0.415 | |
com_dis-mina | 0.457 | 0.017 | 0.149 | |
com_dis | 0.683 | 0.008 | 0.388 | |
com_dis_list | 0.113 | 0.008 | 0.121 | |
com_plot-mina | 24.620 | 0.077 | 3.560 | |
com_plot | 0.219 | 0.001 | 0.213 | |
com_r2-mina | 0.931 | 0.015 | 0.654 | |
com_r2 | 2.148 | 0.041 | 1.493 | |
data-hmp | 0.001 | 0.000 | 0.001 | |
data-maize | 0.001 | 0.000 | 0.000 | |
des_accessor | 0.003 | 0.000 | 0.003 | |
dis_accessor | 0.351 | 0.001 | 0.091 | |
dis_stat_accessor | 32.152 | 0.628 | 31.181 | |
dmr-matrix | 0.804 | 0.008 | 0.473 | |
dmr-mina | 0.764 | 0.017 | 0.483 | |
dmr | 0.792 | 0.000 | 0.462 | |
dmr_accessor | 0.727 | 0.003 | 0.446 | |
fit_tabs-mina | 1.396 | 0.052 | 1.451 | |
fit_tabs | 1.899 | 0.040 | 1.943 | |
get_net_cls_tab-matrix-data.frame-method | 3.450 | 0.004 | 2.835 | |
get_net_cls_tab | 3.699 | 0.005 | 3.061 | |
get_r2-mat | 0.907 | 0.004 | 0.588 | |
get_r2 | 0.866 | 0.001 | 0.617 | |
get_rep-matrix | 0.629 | 0.023 | 0.655 | |
get_rep-mima | 1.466 | 0.011 | 1.480 | |
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 | 0.000 | 0.000 | 0.001 | |
maize_des2 | 0.001 | 0.000 | 0.001 | |
mina-class | 0.001 | 0.000 | 0.001 | |
net_cls-matrix | 3.801 | 0.013 | 3.207 | |
net_cls-mina | 12.025 | 0.047 | 11.488 | |
net_cls | 3.750 | 0.004 | 3.103 | |
net_cls_tab-mina-method | 2.843 | 0.033 | 2.252 | |
net_cls_tab | 3.326 | 0.008 | 2.713 | |
net_dis-mina | 44.738 | 0.690 | 43.093 | |
net_dis | 2.216 | 0.269 | 2.178 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 89.256 | 1.214 | 85.707 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.049 | 0.004 | 0.053 | |
norm_tab-matrix | 1.036 | 0.012 | 1.050 | |
norm_tab-mina | 0.996 | 0.000 | 0.998 | |
norm_tab | 0.054 | 0.000 | 0.055 | |
norm_tab_method_list | 0.061 | 0.006 | 0.068 | |
pcoa_plot | 1.582 | 0.000 | 1.033 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0 | 0 | 0 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0.000 | 0.000 | 0.001 | |