Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:56 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1259/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.10.0 (landing page) Rui Guan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mina.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mina_1.10.0.tar.gz |
StartedAt: 2024-04-16 05:24:00 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 05:30:45 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 405.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mina.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mina_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/mina.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mina/DESCRIPTION’ ... OK * this is package ‘mina’ version ‘1.10.0’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: data 7.4Mb * 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 R 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 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 ... OK * 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 7.4 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 52.269 8.612 59.083 net_dis-mina 26.366 4.681 28.283 com_plot-mina 21.008 3.393 4.156 dis_stat_accessor 20.673 3.135 22.332 net_cls-mina 20.458 0.448 22.444 bs_pm-mina 12.361 1.461 10.621 net_cls 11.062 0.587 11.521 net_cls-matrix 11.108 0.265 12.663 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/mina.Rcheck/00check.log’ for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cp_cor.cpp -o cp_cor.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mina.so RcppExports.o cp_cor.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 | 0.854 | 0.064 | 0.753 | |
adj-mina | 1.108 | 0.059 | 1.001 | |
adj | 1.469 | 0.064 | 1.386 | |
adj_method_list | 0.120 | 0.068 | 0.213 | |
bs_pm-mina | 12.361 | 1.461 | 10.621 | |
bs_pm | 2.490 | 0.316 | 2.910 | |
check_mina | 0.125 | 0.053 | 0.184 | |
check_mina_de | 0.122 | 0.051 | 0.175 | |
check_mina_qu | 0.119 | 0.042 | 0.177 | |
cls_tab | 0.121 | 0.057 | 0.194 | |
com_dis-matrix | 1.836 | 0.017 | 0.643 | |
com_dis-mina | 1.099 | 0.018 | 0.206 | |
com_dis | 1.883 | 0.037 | 0.653 | |
com_dis_list | 0.202 | 0.065 | 0.288 | |
com_plot-mina | 21.008 | 3.393 | 4.156 | |
com_plot | 0.280 | 0.022 | 0.298 | |
com_r2-mina | 2.280 | 0.027 | 1.002 | |
com_r2 | 1.692 | 0.249 | 1.356 | |
data-hmp | 0.003 | 0.003 | 0.005 | |
data-maize | 0.001 | 0.003 | 0.003 | |
des_accessor | 0.005 | 0.002 | 0.006 | |
dis_accessor | 1.433 | 0.030 | 0.168 | |
dis_stat_accessor | 20.673 | 3.135 | 22.332 | |
dmr-matrix | 1.989 | 0.089 | 0.762 | |
dmr-mina | 1.898 | 0.020 | 0.703 | |
dmr | 1.989 | 0.026 | 0.786 | |
dmr_accessor | 2.018 | 0.044 | 0.843 | |
fit_tabs-mina | 1.016 | 0.201 | 1.452 | |
fit_tabs | 1.584 | 0.154 | 2.031 | |
get_net_cls_tab-matrix-data.frame-method | 3.256 | 0.169 | 3.695 | |
get_net_cls_tab | 3.430 | 0.171 | 3.887 | |
get_r2-mat | 2.231 | 0.030 | 1.055 | |
get_r2 | 2.281 | 0.050 | 1.140 | |
get_rep-matrix | 0.496 | 0.033 | 0.621 | |
get_rep-mima | 1.301 | 0.054 | 1.620 | |
hmp_des | 0.001 | 0.002 | 0.004 | |
hmp_otu | 0.002 | 0.002 | 0.003 | |
maize_asv | 0.001 | 0.002 | 0.005 | |
maize_asv2 | 0.002 | 0.002 | 0.006 | |
maize_des | 0.001 | 0.003 | 0.004 | |
maize_des2 | 0.002 | 0.002 | 0.004 | |
mina-class | 0.001 | 0.000 | 0.002 | |
net_cls-matrix | 11.108 | 0.265 | 12.663 | |
net_cls-mina | 20.458 | 0.448 | 22.444 | |
net_cls | 11.062 | 0.587 | 11.521 | |
net_cls_tab-mina-method | 2.739 | 0.044 | 2.537 | |
net_cls_tab | 3.233 | 0.289 | 3.476 | |
net_dis-mina | 26.366 | 4.681 | 28.283 | |
net_dis | 2.345 | 0.425 | 2.583 | |
net_dis_indi | 0.001 | 0.001 | 0.002 | |
net_dis_pcoa | 0.001 | 0.002 | 0.001 | |
net_dis_plot | 52.269 | 8.612 | 59.083 | |
net_grp_cmp | 0.000 | 0.001 | 0.001 | |
net_node_cmp | 0.000 | 0.001 | 0.001 | |
norm_accessor | 0.050 | 0.001 | 0.062 | |
norm_tab-matrix | 1.500 | 0.090 | 1.862 | |
norm_tab-mina | 1.515 | 0.080 | 1.888 | |
norm_tab | 0.051 | 0.001 | 0.058 | |
norm_tab_method_list | 0.104 | 0.045 | 0.184 | |
pcoa_plot | 4.206 | 0.052 | 1.817 | |
sim_par | 0.001 | 0.001 | 0.001 | |
sparcc | 0.001 | 0.001 | 0.001 | |
tab_accessor | 0.000 | 0.001 | 0.005 | |
tina-matrix-method | 0.000 | 0.001 | 0.002 | |
tina | 0.001 | 0.001 | 0.001 | |