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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1263/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.14.0  (landing page)
Rui Guan
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/mina
git_branch: RELEASE_3_20
git_last_commit: f80a036
git_last_commit_date: 2024-10-29 10:53:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for mina on merida1

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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-12-20 06:03:05 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:09:46 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 401.3 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mina.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.14.0’
* 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      51.637  8.660  55.589
net_dis-mina      26.845  4.545  29.742
com_plot-mina     20.455  4.643   4.321
dis_stat_accessor 20.514  3.043  21.517
net_cls-mina      20.372  0.862  22.533
bs_pm-mina        12.546  1.698  11.773
net_cls           10.951  0.285  11.630
net_cls-matrix    10.824  0.220  11.041
* 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

##############################################################################
##############################################################################
###
### 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-matrix0.8270.0740.648
adj-mina1.0730.0740.878
adj1.2810.0701.090
adj_method_list0.1210.0560.178
bs_pm-mina12.546 1.69811.773
bs_pm2.4870.3452.527
check_mina0.0950.0340.130
check_mina_de0.1010.0330.134
check_mina_qu0.0930.0340.127
cls_tab0.1000.0520.156
com_dis-matrix1.9010.0130.592
com_dis-mina1.1330.0200.180
com_dis1.5820.0340.640
com_dis_list0.2060.0610.264
com_plot-mina20.455 4.643 4.321
com_plot0.2750.0150.268
com_r2-mina2.0850.0431.072
com_r21.3640.1211.026
data-hmp0.0020.0020.006
data-maize0.0010.0020.003
des_accessor0.0050.0010.006
dis_accessor1.2460.0260.178
dis_stat_accessor20.514 3.04321.517
dmr-matrix1.7480.0170.687
dmr-mina1.9100.0210.676
dmr1.8220.0970.798
dmr_accessor1.7670.0270.717
fit_tabs-mina1.2620.4151.689
fit_tabs1.6070.2611.898
get_net_cls_tab-matrix-data.frame-method3.2370.2783.343
get_net_cls_tab3.6770.2513.786
get_r2-mat2.0620.1531.154
get_r22.0900.0361.003
get_rep-matrix0.4390.0160.468
get_rep-mima1.2670.0861.368
hmp_des0.0010.0020.003
hmp_otu0.0010.0020.003
maize_asv0.0010.0020.003
maize_asv20.0010.0020.004
maize_des0.0020.0030.004
maize_des20.0010.0030.004
mina-class0.0020.0010.002
net_cls-matrix10.824 0.22011.041
net_cls-mina20.372 0.86222.533
net_cls10.951 0.28511.630
net_cls_tab-mina-method2.8210.0282.811
net_cls_tab3.3590.2463.672
net_dis-mina26.845 4.54529.742
net_dis2.3810.4692.595
net_dis_indi0.0000.0020.002
net_dis_pcoa0.0010.0010.002
net_dis_plot51.637 8.66055.589
net_grp_cmp0.0000.0010.001
net_node_cmp0.0000.0000.001
norm_accessor0.0470.0010.049
norm_tab-matrix1.4710.1281.604
norm_tab-mina1.3890.0571.452
norm_tab0.050.000.05
norm_tab_method_list0.1030.0450.156
pcoa_plot3.8860.0401.553
sim_par0.0010.0010.002
sparcc000
tab_accessor0.0000.0020.002
tina-matrix-method0.0010.0010.002
tina0.0000.0010.001