Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 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" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 1292/2334 | 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: 2025-09-22 22:18:15 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 22:22:37 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 262.2 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: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 14.0.0 (clang-1400.0.29.202)’ * 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 33.699 36.336 35.524 net_dis-mina 17.787 17.532 18.957 dis_stat_accessor 14.168 13.047 14.561 bs_pm-mina 8.656 11.670 7.232 net_cls-mina 19.065 0.583 19.334 com_plot-mina 12.182 3.027 2.253 net_cls 7.109 0.727 7.389 net_cls-matrix 6.499 0.428 6.504 get_net_cls_tab-matrix-data.frame-method 4.701 0.490 4.891 get_net_cls_tab 4.840 0.344 4.802 net_cls_tab 4.806 0.321 4.726 * 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-x86_64/Resources/library’ * installing *source* package ‘mina’ ... ** this is package ‘mina’ version ‘1.17.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cp_cor.cpp -o cp_cor.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 | 0.655 | 0.148 | 0.401 | |
adj-mina | 0.986 | 0.164 | 0.736 | |
adj | 0.895 | 0.059 | 0.643 | |
adj_method_list | 0.078 | 0.053 | 0.178 | |
bs_pm-mina | 8.656 | 11.670 | 7.232 | |
bs_pm | 2.255 | 2.002 | 2.239 | |
check_mina | 0.056 | 0.024 | 0.080 | |
check_mina_de | 0.053 | 0.019 | 0.073 | |
check_mina_qu | 0.058 | 0.022 | 0.082 | |
cls_tab | 0.056 | 0.050 | 0.108 | |
com_dis-matrix | 0.483 | 0.044 | 0.257 | |
com_dis-mina | 0.310 | 0.260 | 0.086 | |
com_dis | 0.481 | 0.067 | 0.264 | |
com_dis_list | 0.116 | 0.107 | 0.192 | |
com_plot-mina | 12.182 | 3.027 | 2.253 | |
com_plot | 0.254 | 0.140 | 0.277 | |
com_r2-mina | 0.754 | 0.114 | 0.531 | |
com_r2 | 0.881 | 0.283 | 0.637 | |
data-hmp | 0.001 | 0.002 | 0.004 | |
data-maize | 0.000 | 0.001 | 0.002 | |
des_accessor | 0.002 | 0.001 | 0.003 | |
dis_accessor | 0.286 | 0.047 | 0.057 | |
dis_stat_accessor | 14.168 | 13.047 | 14.561 | |
dmr-matrix | 0.562 | 0.126 | 0.334 | |
dmr-mina | 0.572 | 0.222 | 0.427 | |
dmr | 0.563 | 0.135 | 0.333 | |
dmr_accessor | 0.566 | 0.134 | 0.342 | |
fit_tabs-mina | 0.734 | 0.229 | 0.977 | |
fit_tabs | 1.160 | 0.344 | 1.531 | |
get_net_cls_tab-matrix-data.frame-method | 4.701 | 0.490 | 4.891 | |
get_net_cls_tab | 4.840 | 0.344 | 4.802 | |
get_r2-mat | 0.669 | 0.332 | 0.453 | |
get_r2 | 0.684 | 0.174 | 0.456 | |
get_rep-matrix | 0.264 | 0.011 | 0.277 | |
get_rep-mima | 0.655 | 0.110 | 0.769 | |
hmp_des | 0.001 | 0.001 | 0.002 | |
hmp_otu | 0.001 | 0.001 | 0.001 | |
maize_asv | 0.000 | 0.001 | 0.002 | |
maize_asv2 | 0.000 | 0.001 | 0.001 | |
maize_des | 0.000 | 0.001 | 0.002 | |
maize_des2 | 0.001 | 0.001 | 0.002 | |
mina-class | 0.002 | 0.000 | 0.002 | |
net_cls-matrix | 6.499 | 0.428 | 6.504 | |
net_cls-mina | 19.065 | 0.583 | 19.334 | |
net_cls | 7.109 | 0.727 | 7.389 | |
net_cls_tab-mina-method | 1.811 | 0.178 | 1.551 | |
net_cls_tab | 4.806 | 0.321 | 4.726 | |
net_dis-mina | 17.787 | 17.532 | 18.957 | |
net_dis | 2.057 | 2.577 | 2.274 | |
net_dis_indi | 0.000 | 0.001 | 0.001 | |
net_dis_pcoa | 0.000 | 0.001 | 0.001 | |
net_dis_plot | 33.699 | 36.336 | 35.524 | |
net_grp_cmp | 0.001 | 0.000 | 0.000 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.031 | 0.001 | 0.031 | |
norm_tab-matrix | 0.641 | 0.165 | 0.811 | |
norm_tab-mina | 0.561 | 0.006 | 0.569 | |
norm_tab | 0.030 | 0.001 | 0.032 | |
norm_tab_method_list | 0.064 | 0.037 | 0.122 | |
pcoa_plot | 1.278 | 0.426 | 0.850 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0.000 | 0.001 | 0.002 | |
tina-matrix-method | 0.000 | 0.001 | 0.001 | |
tina | 0.000 | 0.000 | 0.001 | |