Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 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 1239/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.13.0 (landing page) Rui Guan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
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: 1.13.0 |
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 |
############################################################################## ############################################################################## ### ### 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.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
mina.Rcheck/mina-Ex.timings
name | user | system | elapsed | |
adj-matrix | 0.667 | 0.159 | 0.329 | |
adj-mina | 1.048 | 0.012 | 0.643 | |
adj | 0.947 | 0.002 | 0.378 | |
adj_method_list | 0.060 | 0.002 | 0.065 | |
bs_pm-mina | 13.377 | 1.399 | 6.041 | |
bs_pm | 3.149 | 0.069 | 1.729 | |
check_mina | 0.057 | 0.019 | 0.076 | |
check_mina_de | 0.064 | 0.004 | 0.068 | |
check_mina_qu | 0.064 | 0.004 | 0.068 | |
cls_tab | 0.056 | 0.019 | 0.075 | |
com_dis-matrix | 0.717 | 0.002 | 0.270 | |
com_dis-mina | 0.484 | 0.023 | 0.060 | |
com_dis | 0.738 | 0.005 | 0.275 | |
com_dis_list | 0.093 | 0.003 | 0.096 | |
com_plot-mina | 16.369 | 0.132 | 1.432 | |
com_plot | 0.158 | 0.001 | 0.138 | |
com_r2-mina | 0.784 | 0.085 | 0.497 | |
com_r2 | 1.255 | 0.018 | 0.824 | |
data-hmp | 0.001 | 0.000 | 0.001 | |
data-maize | 0.000 | 0.000 | 0.001 | |
des_accessor | 0.002 | 0.000 | 0.002 | |
dis_accessor | 0.401 | 0.001 | 0.038 | |
dis_stat_accessor | 18.204 | 2.031 | 11.313 | |
dmr-matrix | 0.697 | 0.022 | 0.357 | |
dmr-mina | 0.672 | 0.001 | 0.326 | |
dmr | 0.718 | 0.009 | 0.337 | |
dmr_accessor | 0.685 | 0.000 | 0.340 | |
fit_tabs-mina | 0.774 | 0.028 | 0.802 | |
fit_tabs | 0.887 | 0.041 | 0.928 | |
get_net_cls_tab-matrix-data.frame-method | 1.778 | 0.106 | 1.069 | |
get_net_cls_tab | 1.668 | 0.040 | 1.182 | |
get_r2-mat | 0.835 | 0.213 | 0.458 | |
get_r2 | 0.894 | 0.401 | 0.459 | |
get_rep-matrix | 0.279 | 0.001 | 0.280 | |
get_rep-mima | 0.684 | 0.009 | 0.692 | |
hmp_des | 0.001 | 0.000 | 0.001 | |
hmp_otu | 0.001 | 0.000 | 0.001 | |
maize_asv | 0.001 | 0.000 | 0.001 | |
maize_asv2 | 0.001 | 0.000 | 0.000 | |
maize_des | 0.001 | 0.000 | 0.000 | |
maize_des2 | 0.001 | 0.000 | 0.000 | |
mina-class | 0.001 | 0.000 | 0.000 | |
net_cls-matrix | 6.609 | 0.091 | 6.115 | |
net_cls-mina | 9.880 | 0.048 | 9.264 | |
net_cls | 6.484 | 0.041 | 6.089 | |
net_cls_tab-mina-method | 1.790 | 0.041 | 1.406 | |
net_cls_tab | 1.531 | 0.013 | 1.077 | |
net_dis-mina | 23.052 | 2.039 | 14.570 | |
net_dis | 4.735 | 1.056 | 1.878 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 45.090 | 4.373 | 29.346 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.029 | 0.000 | 0.030 | |
norm_tab-matrix | 0.772 | 0.021 | 0.793 | |
norm_tab-mina | 0.746 | 0.005 | 0.750 | |
norm_tab | 0.028 | 0.000 | 0.028 | |
norm_tab_method_list | 0.056 | 0.000 | 0.056 | |
pcoa_plot | 1.880 | 0.022 | 0.771 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0.001 | 0.000 | 0.000 | |
tab_accessor | 0.000 | 0.000 | 0.001 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0 | 0 | 0 | |