Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1273/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.12.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: mina |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mina_1.12.0.tar.gz |
StartedAt: 2024-06-06 00:55:46 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 01:00:29 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 283.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mina_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mina.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.12.0’ * 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 8.7Mb 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 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 44.615 5.168 30.247 net_dis-mina 23.937 2.202 16.045 dis_stat_accessor 18.846 1.794 12.030 com_plot-mina 16.536 0.089 1.448 bs_pm-mina 13.855 1.652 6.911 net_cls-mina 10.138 0.074 9.710 net_cls-matrix 6.584 0.112 6.255 net_cls 6.460 0.056 6.116 bs_pm 4.728 0.765 1.880 * 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-3.19-bioc/meat/mina.Rcheck/00check.log’ for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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)
mina.Rcheck/mina-Ex.timings
name | user | system | elapsed | |
adj-matrix | 0.661 | 0.057 | 0.344 | |
adj-mina | 1.074 | 0.008 | 0.670 | |
adj | 0.872 | 0.057 | 0.399 | |
adj_method_list | 0.060 | 0.018 | 0.084 | |
bs_pm-mina | 13.855 | 1.652 | 6.911 | |
bs_pm | 4.728 | 0.765 | 1.880 | |
check_mina | 0.073 | 0.012 | 0.085 | |
check_mina_de | 0.076 | 0.000 | 0.076 | |
check_mina_qu | 0.054 | 0.020 | 0.073 | |
cls_tab | 0.064 | 0.011 | 0.076 | |
com_dis-matrix | 0.606 | 0.011 | 0.276 | |
com_dis-mina | 0.400 | 0.013 | 0.064 | |
com_dis | 0.603 | 0.012 | 0.279 | |
com_dis_list | 0.091 | 0.007 | 0.098 | |
com_plot-mina | 16.536 | 0.089 | 1.448 | |
com_plot | 0.139 | 0.018 | 0.141 | |
com_r2-mina | 0.812 | 0.006 | 0.482 | |
com_r2 | 1.262 | 0.009 | 0.844 | |
data-hmp | 0.002 | 0.000 | 0.001 | |
data-maize | 0.001 | 0.000 | 0.001 | |
des_accessor | 0.003 | 0.000 | 0.003 | |
dis_accessor | 0.385 | 0.005 | 0.042 | |
dis_stat_accessor | 18.846 | 1.794 | 12.030 | |
dmr-matrix | 0.706 | 0.020 | 0.364 | |
dmr-mina | 0.691 | 0.004 | 0.344 | |
dmr | 0.721 | 0.001 | 0.357 | |
dmr_accessor | 0.705 | 0.000 | 0.359 | |
fit_tabs-mina | 0.819 | 0.045 | 0.864 | |
fit_tabs | 0.895 | 0.010 | 0.904 | |
get_net_cls_tab-matrix-data.frame-method | 1.483 | 0.025 | 1.083 | |
get_net_cls_tab | 1.773 | 0.010 | 1.275 | |
get_r2-mat | 0.813 | 0.002 | 0.451 | |
get_r2 | 0.813 | 0.017 | 0.467 | |
get_rep-matrix | 0.304 | 0.020 | 0.324 | |
get_rep-mima | 0.725 | 0.009 | 0.733 | |
hmp_des | 0.001 | 0.000 | 0.000 | |
hmp_otu | 0.000 | 0.000 | 0.001 | |
maize_asv | 0.000 | 0.001 | 0.001 | |
maize_asv2 | 0.000 | 0.000 | 0.001 | |
maize_des | 0.000 | 0.001 | 0.000 | |
maize_des2 | 0.000 | 0.001 | 0.001 | |
mina-class | 0.000 | 0.001 | 0.001 | |
net_cls-matrix | 6.584 | 0.112 | 6.255 | |
net_cls-mina | 10.138 | 0.074 | 9.710 | |
net_cls | 6.460 | 0.056 | 6.116 | |
net_cls_tab-mina-method | 1.854 | 0.010 | 1.420 | |
net_cls_tab | 1.808 | 0.090 | 1.115 | |
net_dis-mina | 23.937 | 2.202 | 16.045 | |
net_dis | 4.211 | 0.479 | 2.172 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 44.615 | 5.168 | 30.247 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0.001 | 0.000 | 0.001 | |
norm_accessor | 0.029 | 0.004 | 0.033 | |
norm_tab-matrix | 0.867 | 0.025 | 0.892 | |
norm_tab-mina | 0.836 | 0.001 | 0.838 | |
norm_tab | 0.033 | 0.000 | 0.033 | |
norm_tab_method_list | 0.052 | 0.011 | 0.062 | |
pcoa_plot | 1.571 | 0.013 | 0.770 | |
sim_par | 0.000 | 0.000 | 0.001 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0.001 | 0.000 | 0.000 | |
tina-matrix-method | 0.001 | 0.000 | 0.000 | |
tina | 0.000 | 0.000 | 0.001 | |