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This page was generated on 2024-10-03 11:45 -0400 (Thu, 03 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4461
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4716
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4466
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4498
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4446
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4445
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 1253/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.13.0  (landing page)
Rui Guan
Snapshot Date: 2024-10-02 13:40 -0400 (Wed, 02 Oct 2024)
git_url: https://git.bioconductor.org/packages/mina
git_branch: devel
git_last_commit: 07cc1c7
git_last_commit_date: 2024-04-30 11:29:43 -0400 (Tue, 30 Apr 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2024-10-02 21:49:04 -0400 (Wed, 02 Oct 2024)
EndedAt: 2024-10-02 21:53:09 -0400 (Wed, 02 Oct 2024)
EllapsedTime: 244.5 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_1.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mina.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.13.0’
* 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.sdk’
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.4Mb
* 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 7.4 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      35.693 36.267  37.010
net_dis-mina      19.169 16.478  20.261
dis_stat_accessor 14.506 15.589  14.785
bs_pm-mina         9.003 13.518   7.500
com_plot-mina     12.118  3.162   1.973
net_cls-mina      11.098  0.681  11.280
net_cls-matrix     6.843  0.581   6.944
net_cls            7.025  0.374   6.969
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘mina’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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-matrix0.6240.1540.381
adj-mina0.7990.1660.553
adj0.9750.0500.719
adj_method_list0.0850.1300.158
bs_pm-mina 9.00313.518 7.500
bs_pm2.1102.4182.068
check_mina0.0710.0240.094
check_mina_de0.0660.0210.087
check_mina_qu0.0690.0210.090
cls_tab0.0810.0500.132
com_dis-matrix0.5330.0490.302
com_dis-mina0.3050.1860.071
com_dis0.5140.1160.293
com_dis_list0.1140.1660.170
com_plot-mina12.118 3.162 1.973
com_plot0.1720.1600.164
com_r2-mina0.7830.1880.560
com_r20.9950.2570.695
data-hmp0.0020.0010.003
data-maize0.0010.0010.002
des_accessor0.0030.0010.002
dis_accessor0.3010.0690.084
dis_stat_accessor14.50615.58914.785
dmr-matrix0.6130.1320.380
dmr-mina0.6130.1240.389
dmr0.8660.4750.897
dmr_accessor0.6160.1740.386
fit_tabs-mina0.7090.1450.860
fit_tabs1.0140.2061.229
get_net_cls_tab-matrix-data.frame-method1.6030.4151.560
get_net_cls_tab1.8170.4291.818
get_r2-mat0.7650.1620.543
get_r20.8280.2810.716
get_rep-matrix0.2760.0110.289
get_rep-mima0.7500.0230.777
hmp_des0.0000.0000.001
hmp_otu0.0010.0010.002
maize_asv0.0010.0010.002
maize_asv20.0000.0000.001
maize_des0.0000.0010.002
maize_des20.0010.0010.002
mina-class0.0010.0000.001
net_cls-matrix6.8430.5816.944
net_cls-mina11.098 0.68111.280
net_cls7.0250.3746.969
net_cls_tab-mina-method1.8820.3471.803
net_cls_tab1.6050.1831.336
net_dis-mina19.16916.47820.261
net_dis2.0442.6762.155
net_dis_indi0.0010.0010.000
net_dis_pcoa0.0000.0010.001
net_dis_plot35.69336.26737.010
net_grp_cmp0.0010.0000.000
net_node_cmp000
norm_accessor0.0280.0010.029
norm_tab-matrix0.8120.0100.825
norm_tab-mina1.0030.3281.338
norm_tab0.0350.0010.037
norm_tab_method_list0.0630.0410.131
pcoa_plot1.3250.3800.896
sim_par0.0000.0010.000
sparcc000
tab_accessor0.0010.0000.001
tina-matrix-method000
tina000