Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-01 12:06 -0400 (Wed, 01 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1294/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.17.0 (landing page) Rui Guan
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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. |
Package: mina |
Version: 1.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mina.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mina_1.17.0.tar.gz |
StartedAt: 2025-09-30 20:25:42 -0400 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 20:27:20 -0400 (Tue, 30 Sep 2025) |
EllapsedTime: 98.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mina.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mina_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mina.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mina/DESCRIPTION’ ... OK * this is package ‘mina’ version ‘1.17.0’ * 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking installed package size ... INFO installed size is 8.2Mb sub-directories of 1Mb or more: data 7.6Mb * 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 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 7.6 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 13.475 4.323 14.979 net_dis-mina 6.942 2.305 7.924 net_cls-mina 7.032 0.484 7.624 dis_stat_accessor 5.378 1.553 6.060 net_cls 5.463 0.303 5.751 net_cls-matrix 5.466 0.294 5.630 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/mina.Rcheck/00check.log’ for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘mina’ ... ** this is package ‘mina’ version ‘1.17.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cp_cor.cpp -o cp_cor.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mina.so RcppExports.o cp_cor.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 | 0.322 | 0.024 | 0.153 | |
adj-mina | 0.460 | 0.046 | 0.290 | |
adj | 0.400 | 0.012 | 0.267 | |
adj_method_list | 0.024 | 0.016 | 0.052 | |
bs_pm-mina | 3.111 | 0.520 | 2.562 | |
bs_pm | 0.810 | 0.295 | 0.842 | |
check_mina | 0.018 | 0.006 | 0.028 | |
check_mina_de | 0.017 | 0.005 | 0.021 | |
check_mina_qu | 0.018 | 0.004 | 0.021 | |
cls_tab | 0.020 | 0.009 | 0.028 | |
com_dis-matrix | 0.261 | 0.010 | 0.099 | |
com_dis-mina | 0.225 | 0.008 | 0.048 | |
com_dis | 0.278 | 0.009 | 0.102 | |
com_dis_list | 0.032 | 0.010 | 0.044 | |
com_plot-mina | 3.591 | 0.431 | 0.751 | |
com_plot | 0.074 | 0.019 | 0.086 | |
com_r2-mina | 0.310 | 0.010 | 0.173 | |
com_r2 | 0.315 | 0.059 | 0.260 | |
data-hmp | 0.000 | 0.001 | 0.002 | |
data-maize | 0.001 | 0.001 | 0.000 | |
des_accessor | 0.001 | 0.000 | 0.000 | |
dis_accessor | 0.184 | 0.004 | 0.026 | |
dis_stat_accessor | 5.378 | 1.553 | 6.060 | |
dmr-matrix | 0.273 | 0.010 | 0.134 | |
dmr-mina | 0.284 | 0.030 | 0.151 | |
dmr | 0.280 | 0.012 | 0.125 | |
dmr_accessor | 0.278 | 0.020 | 0.131 | |
fit_tabs-mina | 0.220 | 0.083 | 0.302 | |
fit_tabs | 0.395 | 0.112 | 0.510 | |
get_net_cls_tab-matrix-data.frame-method | 0.717 | 0.081 | 0.606 | |
get_net_cls_tab | 0.740 | 0.083 | 0.639 | |
get_r2-mat | 0.303 | 0.020 | 0.156 | |
get_r2 | 0.307 | 0.023 | 0.156 | |
get_rep-matrix | 0.080 | 0.022 | 0.102 | |
get_rep-mima | 0.223 | 0.053 | 0.278 | |
hmp_des | 0 | 0 | 0 | |
hmp_otu | 0.001 | 0.000 | 0.000 | |
maize_asv | 0.000 | 0.001 | 0.001 | |
maize_asv2 | 0.000 | 0.000 | 0.001 | |
maize_des | 0.000 | 0.001 | 0.001 | |
maize_des2 | 0.000 | 0.000 | 0.001 | |
mina-class | 0 | 0 | 0 | |
net_cls-matrix | 5.466 | 0.294 | 5.630 | |
net_cls-mina | 7.032 | 0.484 | 7.624 | |
net_cls | 5.463 | 0.303 | 5.751 | |
net_cls_tab-mina-method | 1.374 | 0.124 | 1.332 | |
net_cls_tab | 0.728 | 0.083 | 0.628 | |
net_dis-mina | 6.942 | 2.305 | 7.924 | |
net_dis | 0.858 | 0.370 | 0.872 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 13.475 | 4.323 | 14.979 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.011 | 0.003 | 0.013 | |
norm_tab-matrix | 0.221 | 0.026 | 0.248 | |
norm_tab-mina | 0.219 | 0.026 | 0.246 | |
norm_tab | 0.012 | 0.002 | 0.014 | |
norm_tab_method_list | 0.019 | 0.011 | 0.033 | |
pcoa_plot | 0.653 | 0.026 | 0.339 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0 | 0 | 0 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0 | 0 | 0 | |