Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-06 12:04 -0400 (Sat, 06 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1284/2322 | 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 | ERROR | skipped | ||||||||||
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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mina_1.17.0.tar.gz |
StartedAt: 2025-09-06 01:33:59 -0400 (Sat, 06 Sep 2025) |
EndedAt: 2025-09-06 01:39:03 -0400 (Sat, 06 Sep 2025) |
EllapsedTime: 304.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mina_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/mina.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 9.1Mb sub-directories of 1Mb or more: data 7.6Mb libs 1.1Mb * 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 7.6 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 40.366 3.129 28.575 net_dis-mina 19.790 1.143 14.070 com_plot-mina 17.169 0.069 1.327 dis_stat_accessor 15.501 1.460 11.661 net_cls-mina 13.499 0.159 13.204 bs_pm-mina 11.155 1.105 6.180 net_cls-matrix 6.446 0.185 6.090 net_cls 6.413 0.047 6.038 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/mina.Rcheck/00check.log’ for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘mina’ ... ** this is package ‘mina’ version ‘1.17.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:4: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cp_cor.cpp -o cp_cor.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/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 | 0.580 | 0.051 | 0.268 | |
adj-mina | 0.960 | 0.026 | 0.601 | |
adj | 1.003 | 0.006 | 0.577 | |
adj_method_list | 0.060 | 0.008 | 0.072 | |
bs_pm-mina | 11.155 | 1.105 | 6.180 | |
bs_pm | 3.054 | 0.143 | 1.702 | |
check_mina | 0.058 | 0.009 | 0.066 | |
check_mina_de | 0.054 | 0.008 | 0.062 | |
check_mina_qu | 0.056 | 0.005 | 0.061 | |
cls_tab | 0.056 | 0.003 | 0.059 | |
com_dis-matrix | 0.505 | 0.010 | 0.201 | |
com_dis-mina | 0.383 | 0.004 | 0.050 | |
com_dis | 0.556 | 0.012 | 0.219 | |
com_dis_list | 0.087 | 0.012 | 0.097 | |
com_plot-mina | 17.169 | 0.069 | 1.327 | |
com_plot | 0.149 | 0.007 | 0.101 | |
com_r2-mina | 0.658 | 0.006 | 0.385 | |
com_r2 | 0.853 | 0.007 | 0.441 | |
data-hmp | 0.000 | 0.001 | 0.001 | |
data-maize | 0 | 0 | 0 | |
des_accessor | 0.002 | 0.000 | 0.002 | |
dis_accessor | 0.329 | 0.002 | 0.035 | |
dis_stat_accessor | 15.501 | 1.460 | 11.661 | |
dmr-matrix | 0.623 | 0.011 | 0.295 | |
dmr-mina | 0.620 | 0.004 | 0.271 | |
dmr | 0.608 | 0.004 | 0.277 | |
dmr_accessor | 0.605 | 0.008 | 0.281 | |
fit_tabs-mina | 0.501 | 0.082 | 0.583 | |
fit_tabs | 0.772 | 0.051 | 0.824 | |
get_net_cls_tab-matrix-data.frame-method | 2.274 | 0.011 | 1.741 | |
get_net_cls_tab | 2.502 | 0.015 | 2.084 | |
get_r2-mat | 0.712 | 0.015 | 0.378 | |
get_r2 | 0.705 | 0.007 | 0.393 | |
get_rep-matrix | 0.256 | 0.003 | 0.260 | |
get_rep-mima | 0.588 | 0.007 | 0.596 | |
hmp_des | 0 | 0 | 0 | |
hmp_otu | 0 | 0 | 0 | |
maize_asv | 0 | 0 | 0 | |
maize_asv2 | 0.000 | 0.001 | 0.000 | |
maize_des | 0.000 | 0.000 | 0.001 | |
maize_des2 | 0.000 | 0.000 | 0.001 | |
mina-class | 0.001 | 0.000 | 0.001 | |
net_cls-matrix | 6.446 | 0.185 | 6.090 | |
net_cls-mina | 13.499 | 0.159 | 13.204 | |
net_cls | 6.413 | 0.047 | 6.038 | |
net_cls_tab-mina-method | 1.747 | 0.014 | 1.304 | |
net_cls_tab | 2.309 | 0.008 | 1.856 | |
net_dis-mina | 19.790 | 1.143 | 14.070 | |
net_dis | 3.066 | 0.225 | 1.791 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 40.366 | 3.129 | 28.575 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.025 | 0.003 | 0.028 | |
norm_tab-matrix | 0.601 | 0.030 | 0.632 | |
norm_tab-mina | 0.588 | 0.008 | 0.597 | |
norm_tab | 0.025 | 0.000 | 0.025 | |
norm_tab_method_list | 0.054 | 0.007 | 0.062 | |
pcoa_plot | 1.366 | 0.006 | 0.677 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0 | 0 | 0 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0 | 0 | 0 | |