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This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1239/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.13.0  (landing page)
Rui Guan
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 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)
nebbiolo2Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 1.13.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mina_1.13.0.tar.gz
StartedAt: 2024-06-25 00:47:35 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 00:52:17 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 282.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mina.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mina_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mina.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
    libs   1.2Mb
* 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      45.090  4.373  29.346
net_dis-mina      23.052  2.039  14.570
dis_stat_accessor 18.204  2.031  11.313
com_plot-mina     16.369  0.132   1.432
bs_pm-mina        13.377  1.399   6.041
net_cls-mina       9.880  0.048   9.264
net_cls-matrix     6.609  0.091   6.115
net_cls            6.484  0.041   6.089
net_dis            4.735  1.056   1.878
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/mina.Rcheck/00check.log’
for details.


Installation output

mina.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mina
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘mina’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c cp_cor.cpp -o cp_cor.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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-matrix0.6670.1590.329
adj-mina1.0480.0120.643
adj0.9470.0020.378
adj_method_list0.0600.0020.065
bs_pm-mina13.377 1.399 6.041
bs_pm3.1490.0691.729
check_mina0.0570.0190.076
check_mina_de0.0640.0040.068
check_mina_qu0.0640.0040.068
cls_tab0.0560.0190.075
com_dis-matrix0.7170.0020.270
com_dis-mina0.4840.0230.060
com_dis0.7380.0050.275
com_dis_list0.0930.0030.096
com_plot-mina16.369 0.132 1.432
com_plot0.1580.0010.138
com_r2-mina0.7840.0850.497
com_r21.2550.0180.824
data-hmp0.0010.0000.001
data-maize0.0000.0000.001
des_accessor0.0020.0000.002
dis_accessor0.4010.0010.038
dis_stat_accessor18.204 2.03111.313
dmr-matrix0.6970.0220.357
dmr-mina0.6720.0010.326
dmr0.7180.0090.337
dmr_accessor0.6850.0000.340
fit_tabs-mina0.7740.0280.802
fit_tabs0.8870.0410.928
get_net_cls_tab-matrix-data.frame-method1.7780.1061.069
get_net_cls_tab1.6680.0401.182
get_r2-mat0.8350.2130.458
get_r20.8940.4010.459
get_rep-matrix0.2790.0010.280
get_rep-mima0.6840.0090.692
hmp_des0.0010.0000.001
hmp_otu0.0010.0000.001
maize_asv0.0010.0000.001
maize_asv20.0010.0000.000
maize_des0.0010.0000.000
maize_des20.0010.0000.000
mina-class0.0010.0000.000
net_cls-matrix6.6090.0916.115
net_cls-mina9.8800.0489.264
net_cls6.4840.0416.089
net_cls_tab-mina-method1.7900.0411.406
net_cls_tab1.5310.0131.077
net_dis-mina23.052 2.03914.570
net_dis4.7351.0561.878
net_dis_indi000
net_dis_pcoa000
net_dis_plot45.090 4.37329.346
net_grp_cmp000
net_node_cmp000
norm_accessor0.0290.0000.030
norm_tab-matrix0.7720.0210.793
norm_tab-mina0.7460.0050.750
norm_tab0.0280.0000.028
norm_tab_method_list0.0560.0000.056
pcoa_plot1.8800.0220.771
sim_par000
sparcc0.0010.0000.000
tab_accessor0.0000.0000.001
tina-matrix-method000
tina000