Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 2024-07-22 02:17:56 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 02:22:22 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 265.5 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 4.4.1 (2024-06-14) * 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 39.667 3.235 26.807 net_dis-mina 21.285 2.093 13.827 dis_stat_accessor 15.322 1.966 10.587 com_plot-mina 17.078 0.088 1.418 bs_pm-mina 11.297 1.206 5.599 net_cls-mina 9.638 0.117 9.362 net_cls 6.493 0.060 6.084 net_cls-matrix 6.410 0.074 6.044 * 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 | 0.641 | 0.090 | 0.330 | |
adj-mina | 1.026 | 0.024 | 0.632 | |
adj | 0.795 | 0.000 | 0.383 | |
adj_method_list | 0.059 | 0.010 | 0.071 | |
bs_pm-mina | 11.297 | 1.206 | 5.599 | |
bs_pm | 3.443 | 0.496 | 1.589 | |
check_mina | 0.056 | 0.012 | 0.068 | |
check_mina_de | 0.055 | 0.016 | 0.070 | |
check_mina_qu | 0.056 | 0.012 | 0.067 | |
cls_tab | 0.058 | 0.012 | 0.070 | |
com_dis-matrix | 0.584 | 0.006 | 0.253 | |
com_dis-mina | 0.385 | 0.000 | 0.052 | |
com_dis | 0.602 | 0.000 | 0.256 | |
com_dis_list | 0.086 | 0.006 | 0.093 | |
com_plot-mina | 17.078 | 0.088 | 1.418 | |
com_plot | 0.169 | 0.002 | 0.134 | |
com_r2-mina | 0.825 | 0.000 | 0.469 | |
com_r2 | 1.198 | 0.010 | 0.761 | |
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 | 0.388 | 0.002 | 0.039 | |
dis_stat_accessor | 15.322 | 1.966 | 10.587 | |
dmr-matrix | 0.658 | 0.011 | 0.332 | |
dmr-mina | 0.658 | 0.009 | 0.333 | |
dmr | 0.675 | 0.045 | 0.328 | |
dmr_accessor | 0.676 | 0.005 | 0.342 | |
fit_tabs-mina | 0.768 | 0.077 | 0.846 | |
fit_tabs | 0.952 | 0.025 | 0.977 | |
get_net_cls_tab-matrix-data.frame-method | 1.489 | 0.012 | 1.051 | |
get_net_cls_tab | 1.587 | 0.007 | 1.154 | |
get_r2-mat | 0.794 | 0.000 | 0.428 | |
get_r2 | 0.797 | 0.035 | 0.463 | |
get_rep-matrix | 0.269 | 0.001 | 0.269 | |
get_rep-mima | 0.683 | 0.000 | 0.683 | |
hmp_des | 0.000 | 0.001 | 0.001 | |
hmp_otu | 0.000 | 0.001 | 0.001 | |
maize_asv | 0.000 | 0.001 | 0.001 | |
maize_asv2 | 0.001 | 0.000 | 0.000 | |
maize_des | 0.000 | 0.000 | 0.001 | |
maize_des2 | 0.001 | 0.000 | 0.001 | |
mina-class | 0.001 | 0.000 | 0.001 | |
net_cls-matrix | 6.410 | 0.074 | 6.044 | |
net_cls-mina | 9.638 | 0.117 | 9.362 | |
net_cls | 6.493 | 0.060 | 6.084 | |
net_cls_tab-mina-method | 1.804 | 0.021 | 1.414 | |
net_cls_tab | 1.528 | 0.010 | 1.082 | |
net_dis-mina | 21.285 | 2.093 | 13.827 | |
net_dis | 3.506 | 0.892 | 1.614 | |
net_dis_indi | 0.001 | 0.000 | 0.001 | |
net_dis_pcoa | 0.001 | 0.000 | 0.001 | |
net_dis_plot | 39.667 | 3.235 | 26.807 | |
net_grp_cmp | 0.000 | 0.000 | 0.001 | |
net_node_cmp | 0.001 | 0.000 | 0.000 | |
norm_accessor | 0.029 | 0.000 | 0.028 | |
norm_tab-matrix | 0.768 | 0.008 | 0.776 | |
norm_tab-mina | 0.737 | 0.004 | 0.741 | |
norm_tab | 0.022 | 0.003 | 0.026 | |
norm_tab_method_list | 0.048 | 0.010 | 0.058 | |
pcoa_plot | 1.461 | 0.009 | 0.751 | |
sim_par | 0.001 | 0.000 | 0.001 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0 | 0 | 0 | |
tina-matrix-method | 0 | 0 | 0 | |
tina | 0 | 0 | 0 | |