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This page was generated on 2025-10-03 12:06 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1294/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.17.0  (landing page)
Rui Guan
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 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 kjohnson3

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: 2025-10-02 20:48:44 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 20:50:22 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 98.1 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
###
##############################################################################
##############################################################################


* 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      13.376  4.453  14.815
net_dis-mina       6.925  2.379   7.913
net_cls-mina       6.968  0.476   7.455
dis_stat_accessor  5.436  1.501   5.825
net_cls            5.516  0.287   5.633
net_cls-matrix     5.492  0.278   5.834
* 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-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)

Tests output


Example timings

mina.Rcheck/mina-Ex.timings

nameusersystemelapsed
adj-matrix0.3320.0180.154
adj-mina0.4600.0160.296
adj0.4070.0160.241
adj_method_list0.0240.0140.049
bs_pm-mina3.1300.5532.562
bs_pm0.7570.2670.774
check_mina0.0190.0060.024
check_mina_de0.0170.0040.022
check_mina_qu0.0170.0040.021
cls_tab0.0200.0100.029
com_dis-matrix0.2420.0100.099
com_dis-mina0.2110.0040.043
com_dis0.2760.0070.096
com_dis_list0.0300.0130.048
com_plot-mina3.6770.6430.771
com_plot0.0730.0160.079
com_r2-mina0.3240.0200.176
com_r20.3180.0560.241
data-hmp0.0010.0000.001
data-maize0.0000.0000.001
des_accessor0.0010.0000.001
dis_accessor0.1870.0060.028
dis_stat_accessor5.4361.5015.825
dmr-matrix0.2880.0130.144
dmr-mina0.2910.0230.151
dmr0.2730.0120.135
dmr_accessor0.2790.0110.124
fit_tabs-mina0.2190.0760.296
fit_tabs0.3860.1130.503
get_net_cls_tab-matrix-data.frame-method0.7050.0810.606
get_net_cls_tab0.7480.0830.650
get_r2-mat0.3160.0090.157
get_r20.3030.0160.156
get_rep-matrix0.0810.0200.101
get_rep-mima0.2260.0590.294
hmp_des0.0000.0000.001
hmp_otu0.0010.0010.001
maize_asv000
maize_asv20.0000.0010.000
maize_des0.0000.0000.001
maize_des20.0010.0000.000
mina-class0.0000.0010.000
net_cls-matrix5.4920.2785.834
net_cls-mina6.9680.4767.455
net_cls5.5160.2875.633
net_cls_tab-mina-method1.3660.1121.317
net_cls_tab0.7310.0880.635
net_dis-mina6.9252.3797.913
net_dis0.8310.3550.848
net_dis_indi000
net_dis_pcoa0.0000.0010.000
net_dis_plot13.376 4.45314.815
net_grp_cmp000
net_node_cmp000
norm_accessor0.0110.0020.012
norm_tab-matrix0.2220.0190.250
norm_tab-mina0.2180.0280.258
norm_tab0.0110.0020.013
norm_tab_method_list0.0210.0140.037
pcoa_plot0.6480.0310.388
sim_par000
sparcc000
tab_accessor000
tina-matrix-method000
tina000