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This page was generated on 2025-09-24 12:05 -0400 (Wed, 24 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4827
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4614
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4558
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1292/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.17.0  (landing page)
Rui Guan
Snapshot Date: 2025-09-23 13:45 -0400 (Tue, 23 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    OK    ERROR  


CHECK results for mina on lconway

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: /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: 2025-09-23 22:23:45 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 22:28:08 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 262.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mina.Rcheck
Warnings: 1

Command output

##############################################################################
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### 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
###
##############################################################################
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* 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                             33.837 37.321  35.490
net_dis-mina                             17.853 20.314  19.007
dis_stat_accessor                        14.403 13.647  14.707
bs_pm-mina                                8.556 12.915   7.067
net_cls-mina                             19.702  0.685  19.910
com_plot-mina                            12.494  3.646   2.221
net_cls                                   7.043  0.582   7.273
net_cls-matrix                            6.578  0.401   6.547
net_dis                                   2.116  3.570   2.262
get_net_cls_tab-matrix-data.frame-method  4.682  0.485   4.656
get_net_cls_tab                           4.811  0.338   4.729
* 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.


Installation output

mina.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

mina.Rcheck/mina-Ex.timings

nameusersystemelapsed
adj-matrix0.6610.1010.409
adj-mina1.0160.2650.769
adj0.9380.0500.691
adj_method_list0.0830.1260.189
bs_pm-mina 8.55612.915 7.067
bs_pm2.2352.3442.221
check_mina0.0580.0250.083
check_mina_de0.0540.0200.074
check_mina_qu0.0560.0210.077
cls_tab0.0590.0500.110
com_dis-matrix0.4840.0620.254
com_dis-mina0.3120.1070.084
com_dis0.4790.1390.259
com_dis_list0.1060.1100.174
com_plot-mina12.494 3.646 2.221
com_plot0.2430.1520.247
com_r2-mina0.7150.2190.486
com_r20.8960.3250.643
data-hmp0.0010.0020.003
data-maize0.0010.0010.002
des_accessor0.0020.0000.002
dis_accessor0.2870.1100.050
dis_stat_accessor14.40313.64714.707
dmr-matrix0.5410.1380.310
dmr-mina0.5650.1920.407
dmr0.5560.1560.326
dmr_accessor0.5520.2120.334
fit_tabs-mina0.6830.2090.901
fit_tabs1.1600.3491.527
get_net_cls_tab-matrix-data.frame-method4.6820.4854.656
get_net_cls_tab4.8110.3384.729
get_r2-mat0.7050.1310.479
get_r20.7020.1360.478
get_rep-matrix0.2500.0110.263
get_rep-mima0.6640.1180.798
hmp_des0.0000.0010.001
hmp_otu0.0010.0020.002
maize_asv0.0000.0020.002
maize_asv20.0010.0010.001
maize_des0.0010.0010.001
maize_des20.0000.0020.001
mina-class0.0010.0000.001
net_cls-matrix6.5780.4016.547
net_cls-mina19.702 0.68519.910
net_cls7.0430.5827.273
net_cls_tab-mina-method1.7580.1751.495
net_cls_tab4.6600.3064.553
net_dis-mina17.85320.31419.007
net_dis2.1163.5702.262
net_dis_indi0.0000.0010.001
net_dis_pcoa0.0010.0000.001
net_dis_plot33.83737.32135.490
net_grp_cmp000
net_node_cmp000
norm_accessor0.0310.0010.033
norm_tab-matrix0.6730.1390.817
norm_tab-mina0.6370.0040.644
norm_tab0.0320.0010.032
norm_tab_method_list0.0640.0380.128
pcoa_plot1.3590.4080.936
sim_par0.0000.0000.001
sparcc000
tab_accessor0.0010.0010.001
tina-matrix-method0.0000.0010.001
tina0.0000.0010.000