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 11:39 -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: /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_1.13.0.tar.gz |
StartedAt: 2024-06-24 21:26:30 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 21:30:27 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 237.7 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mina.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-apple-darwin20 * 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 ‘1.13.0’ * 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: ‘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 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 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 7.4 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 35.009 40.874 36.214 net_dis-mina 18.440 21.689 19.328 dis_stat_accessor 14.532 16.675 14.803 bs_pm-mina 8.886 16.376 7.370 com_plot-mina 12.377 2.755 2.017 net_cls-mina 11.254 0.811 11.640 net_cls-matrix 6.939 0.425 6.951 net_cls 6.524 0.605 6.661 net_dis 1.964 3.324 2.048 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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 | 0.617 | 0.158 | 0.361 | |
adj-mina | 0.770 | 0.310 | 0.514 | |
adj | 0.950 | 0.055 | 0.689 | |
adj_method_list | 0.083 | 0.146 | 0.154 | |
bs_pm-mina | 8.886 | 16.376 | 7.370 | |
bs_pm | 2.084 | 2.795 | 2.049 | |
check_mina | 0.071 | 0.025 | 0.096 | |
check_mina_de | 0.068 | 0.022 | 0.089 | |
check_mina_qu | 0.064 | 0.020 | 0.083 | |
cls_tab | 0.070 | 0.050 | 0.121 | |
com_dis-matrix | 0.532 | 0.046 | 0.300 | |
com_dis-mina | 0.300 | 0.116 | 0.071 | |
com_dis | 0.531 | 0.115 | 0.301 | |
com_dis_list | 0.116 | 0.123 | 0.179 | |
com_plot-mina | 12.377 | 2.755 | 2.017 | |
com_plot | 0.177 | 0.165 | 0.167 | |
com_r2-mina | 0.771 | 0.179 | 0.548 | |
com_r2 | 0.984 | 0.228 | 0.683 | |
data-hmp | 0.001 | 0.001 | 0.002 | |
data-maize | 0.000 | 0.001 | 0.002 | |
des_accessor | 0.002 | 0.000 | 0.003 | |
dis_accessor | 0.298 | 0.057 | 0.071 | |
dis_stat_accessor | 14.532 | 16.675 | 14.803 | |
dmr-matrix | 0.613 | 0.151 | 0.374 | |
dmr-mina | 0.583 | 0.166 | 0.358 | |
dmr | 0.599 | 0.137 | 0.378 | |
dmr_accessor | 0.635 | 0.242 | 0.490 | |
fit_tabs-mina | 0.757 | 0.181 | 0.945 | |
fit_tabs | 0.988 | 0.113 | 1.119 | |
get_net_cls_tab-matrix-data.frame-method | 1.662 | 0.422 | 1.550 | |
get_net_cls_tab | 1.689 | 0.343 | 1.547 | |
get_r2-mat | 0.714 | 0.149 | 0.478 | |
get_r2 | 0.758 | 0.188 | 0.568 | |
get_rep-matrix | 0.275 | 0.009 | 0.286 | |
get_rep-mima | 0.836 | 0.097 | 0.938 | |
hmp_des | 0.001 | 0.001 | 0.003 | |
hmp_otu | 0.001 | 0.001 | 0.002 | |
maize_asv | 0.001 | 0.002 | 0.002 | |
maize_asv2 | 0.001 | 0.001 | 0.002 | |
maize_des | 0.001 | 0.002 | 0.002 | |
maize_des2 | 0.001 | 0.001 | 0.001 | |
mina-class | 0.000 | 0.001 | 0.001 | |
net_cls-matrix | 6.939 | 0.425 | 6.951 | |
net_cls-mina | 11.254 | 0.811 | 11.640 | |
net_cls | 6.524 | 0.605 | 6.661 | |
net_cls_tab-mina-method | 1.732 | 0.246 | 1.464 | |
net_cls_tab | 1.396 | 0.418 | 1.286 | |
net_dis-mina | 18.440 | 21.689 | 19.328 | |
net_dis | 1.964 | 3.324 | 2.048 | |
net_dis_indi | 0.000 | 0.001 | 0.000 | |
net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
net_dis_plot | 35.009 | 40.874 | 36.214 | |
net_grp_cmp | 0.001 | 0.000 | 0.000 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.030 | 0.001 | 0.030 | |
norm_tab-matrix | 0.801 | 0.009 | 0.815 | |
norm_tab-mina | 0.767 | 0.034 | 0.805 | |
norm_tab | 0.03 | 0.00 | 0.03 | |
norm_tab_method_list | 0.059 | 0.035 | 0.115 | |
pcoa_plot | 1.285 | 0.477 | 0.870 | |
sim_par | 0 | 0 | 0 | |
sparcc | 0.000 | 0.000 | 0.001 | |
tab_accessor | 0.000 | 0.001 | 0.001 | |
tina-matrix-method | 0.000 | 0.001 | 0.000 | |
tina | 0.000 | 0.001 | 0.001 | |