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This page was generated on 2025-09-26 12:03 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1292/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.17.0  (landing page)
Rui Guan
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/mina
git_branch: devel
git_last_commit: c503615
git_last_commit_date: 2025-04-15 12:15:34 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for mina on nebbiolo2

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.

raw results


Summary

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: 2025-09-26 01:35:43 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 01:40:32 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 289.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mina.Rcheck
Warnings: 1

Command output

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### 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
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/mina.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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      38.476  2.749  27.174
net_dis-mina      20.976  1.967  14.587
com_plot-mina     16.085  0.100   1.813
dis_stat_accessor 14.678  1.398  10.733
net_cls-mina      13.381  0.004  12.863
bs_pm-mina        10.712  1.215   5.803
net_cls            6.471  0.067   6.065
net_cls-matrix     6.521  0.014   6.028
* 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.


Installation output

mina.Rcheck/00install.out

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###
### 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
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)

Tests output


Example timings

mina.Rcheck/mina-Ex.timings

nameusersystemelapsed
adj-matrix0.6450.0550.337
adj-mina0.9500.0090.579
adj0.7800.0770.337
adj_method_list0.0640.0070.074
bs_pm-mina10.712 1.215 5.803
bs_pm3.0610.1881.783
check_mina0.0540.0190.073
check_mina_de0.0520.0080.060
check_mina_qu0.0560.0110.067
cls_tab0.0580.0030.061
com_dis-matrix0.5340.0020.200
com_dis-mina0.3860.0050.054
com_dis0.5470.0070.207
com_dis_list0.0880.0070.094
com_plot-mina16.085 0.100 1.813
com_plot0.2000.0050.181
com_r2-mina0.6750.0010.402
com_r20.8380.0100.462
data-hmp0.0020.0000.001
data-maize0.0010.0000.001
des_accessor0.0020.0000.002
dis_accessor0.5530.0020.278
dis_stat_accessor14.678 1.39810.733
dmr-matrix0.6000.0290.289
dmr-mina0.6220.0040.277
dmr0.5900.0010.286
dmr_accessor0.5650.0010.274
fit_tabs-mina0.7700.0150.785
fit_tabs0.7550.0000.756
get_net_cls_tab-matrix-data.frame-method2.1780.0291.718
get_net_cls_tab2.3700.0061.865
get_r2-mat0.7260.0010.359
get_r20.6500.0020.357
get_rep-matrix0.2700.0010.271
get_rep-mima0.5650.0000.566
hmp_des0.0000.0000.001
hmp_otu000
maize_asv000
maize_asv2000
maize_des0.0000.0000.001
maize_des20.0000.0000.001
mina-class0.0000.0010.001
net_cls-matrix6.5210.0146.028
net_cls-mina13.381 0.00412.863
net_cls6.4710.0676.065
net_cls_tab-mina-method1.7920.0421.346
net_cls_tab2.3630.0251.885
net_dis-mina20.976 1.96714.587
net_dis3.0160.2381.873
net_dis_indi000
net_dis_pcoa000
net_dis_plot38.476 2.74927.174
net_grp_cmp000
net_node_cmp000
norm_accessor0.0240.0000.024
norm_tab-matrix0.5770.0140.590
norm_tab-mina0.5640.0030.567
norm_tab0.0240.0000.025
norm_tab_method_list0.0540.0050.058
pcoa_plot1.4170.0110.756
sim_par000
sparcc000
tab_accessor0.0000.0000.001
tina-matrix-method000
tina0.0000.0000.001