Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 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" | 4685 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4400 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4349 |
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: 2024-06-15 00:52:27 -0400 (Sat, 15 Jun 2024) |
EndedAt: 2024-06-15 00:57:02 -0400 (Sat, 15 Jun 2024) |
EllapsedTime: 274.4 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 46.679 3.626 30.385 net_dis-mina 24.423 2.597 16.310 dis_stat_accessor 19.149 1.930 13.050 bs_pm-mina 14.625 1.909 6.776 com_plot-mina 15.901 0.009 1.519 net_cls-mina 10.155 0.084 9.787 net_cls 6.602 0.035 6.177 net_cls-matrix 6.580 0.038 6.168 net_dis 4.671 0.650 2.119 * 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 | 0.655 | 0.036 | 0.332 | |
adj-mina | 1.078 | 0.007 | 0.658 | |
adj | 0.909 | 0.007 | 0.418 | |
adj_method_list | 0.058 | 0.013 | 0.074 | |
bs_pm-mina | 14.625 | 1.909 | 6.776 | |
bs_pm | 4.001 | 0.812 | 1.953 | |
check_mina | 0.071 | 0.017 | 0.088 | |
check_mina_de | 0.063 | 0.012 | 0.076 | |
check_mina_qu | 0.066 | 0.004 | 0.070 | |
cls_tab | 0.065 | 0.016 | 0.081 | |
com_dis-matrix | 0.647 | 0.001 | 0.284 | |
com_dis-mina | 0.391 | 0.012 | 0.063 | |
com_dis | 0.654 | 0.006 | 0.281 | |
com_dis_list | 0.094 | 0.003 | 0.097 | |
com_plot-mina | 15.901 | 0.009 | 1.519 | |
com_plot | 0.163 | 0.005 | 0.147 | |
com_r2-mina | 0.866 | 0.000 | 0.529 | |
com_r2 | 1.262 | 0.000 | 0.839 | |
data-hmp | 0.002 | 0.000 | 0.002 | |
data-maize | 0.001 | 0.000 | 0.001 | |
des_accessor | 0.003 | 0.000 | 0.004 | |
dis_accessor | 0.376 | 0.000 | 0.046 | |
dis_stat_accessor | 19.149 | 1.930 | 13.050 | |
dmr-matrix | 0.714 | 0.015 | 0.353 | |
dmr-mina | 0.714 | 0.000 | 0.333 | |
dmr | 0.681 | 0.012 | 0.338 | |
dmr_accessor | 0.711 | 0.000 | 0.360 | |
fit_tabs-mina | 0.794 | 0.005 | 0.799 | |
fit_tabs | 0.891 | 0.000 | 0.892 | |
get_net_cls_tab-matrix-data.frame-method | 1.671 | 0.058 | 1.096 | |
get_net_cls_tab | 1.681 | 0.009 | 1.229 | |
get_r2-mat | 0.849 | 0.033 | 0.500 | |
get_r2 | 0.843 | 0.013 | 0.491 | |
get_rep-matrix | 0.301 | 0.008 | 0.309 | |
get_rep-mima | 0.736 | 0.007 | 0.743 | |
hmp_des | 0.001 | 0.000 | 0.001 | |
hmp_otu | 0.000 | 0.000 | 0.001 | |
maize_asv | 0.000 | 0.000 | 0.001 | |
maize_asv2 | 0.000 | 0.000 | 0.001 | |
maize_des | 0.000 | 0.000 | 0.001 | |
maize_des2 | 0.000 | 0.000 | 0.001 | |
mina-class | 0.000 | 0.000 | 0.001 | |
net_cls-matrix | 6.580 | 0.038 | 6.168 | |
net_cls-mina | 10.155 | 0.084 | 9.787 | |
net_cls | 6.602 | 0.035 | 6.177 | |
net_cls_tab-mina-method | 1.872 | 0.036 | 1.461 | |
net_cls_tab | 1.623 | 0.001 | 1.140 | |
net_dis-mina | 24.423 | 2.597 | 16.310 | |
net_dis | 4.671 | 0.650 | 2.119 | |
net_dis_indi | 0 | 0 | 0 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 46.679 | 3.626 | 30.385 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.029 | 0.000 | 0.029 | |
norm_tab-matrix | 0.795 | 0.027 | 0.823 | |
norm_tab-mina | 0.79 | 0.00 | 0.79 | |
norm_tab | 0.027 | 0.000 | 0.028 | |
norm_tab_method_list | 0.051 | 0.006 | 0.058 | |
pcoa_plot | 1.435 | 0.009 | 0.777 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0.001 | 0.000 | 0.000 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0 | 0 | 0 | |