Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 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" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1238/2239 | 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 | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 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: 1.13.0 |
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: 2024-06-11 01:16:43 -0400 (Tue, 11 Jun 2024) |
EndedAt: 2024-06-11 01:21:17 -0400 (Tue, 11 Jun 2024) |
EllapsedTime: 273.5 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 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * 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 15.0.0 (clang-1500.0.40.1)’ * 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 38.226 9.726 44.714 net_dis-mina 18.936 4.651 21.976 net_cls-mina 19.089 1.005 19.743 dis_stat_accessor 15.426 2.879 17.127 net_cls-matrix 16.658 0.870 17.195 net_cls 16.664 0.498 16.838 com_plot-mina 8.178 1.855 2.987 bs_pm-mina 7.687 0.614 7.181 * 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-arm64/Resources/library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cp_cor.cpp -o cp_cor.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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 | 0.719 | 0.035 | 0.406 | |
adj-mina | 1.117 | 0.024 | 0.799 | |
adj | 0.871 | 0.044 | 0.573 | |
adj_method_list | 0.076 | 0.037 | 0.133 | |
bs_pm-mina | 7.687 | 0.614 | 7.181 | |
bs_pm | 2.074 | 0.232 | 2.133 | |
check_mina | 0.089 | 0.017 | 0.106 | |
check_mina_de | 0.084 | 0.014 | 0.099 | |
check_mina_qu | 0.085 | 0.015 | 0.098 | |
cls_tab | 0.091 | 0.025 | 0.116 | |
com_dis-matrix | 0.680 | 0.022 | 0.365 | |
com_dis-mina | 0.452 | 0.019 | 0.137 | |
com_dis | 0.679 | 0.021 | 0.371 | |
com_dis_list | 0.094 | 0.036 | 0.135 | |
com_plot-mina | 8.178 | 1.855 | 2.987 | |
com_plot | 0.170 | 0.006 | 0.171 | |
com_r2-mina | 0.916 | 0.031 | 0.610 | |
com_r2 | 1.251 | 0.179 | 1.098 | |
data-hmp | 0.002 | 0.001 | 0.003 | |
data-maize | 0.001 | 0.001 | 0.002 | |
des_accessor | 0.003 | 0.000 | 0.003 | |
dis_accessor | 0.444 | 0.016 | 0.129 | |
dis_stat_accessor | 15.426 | 2.879 | 17.127 | |
dmr-matrix | 0.790 | 0.021 | 0.474 | |
dmr-mina | 0.800 | 0.017 | 0.479 | |
dmr | 0.817 | 0.044 | 0.524 | |
dmr_accessor | 0.795 | 0.023 | 0.479 | |
fit_tabs-mina | 0.970 | 0.269 | 1.239 | |
fit_tabs | 1.021 | 0.173 | 1.194 | |
get_net_cls_tab-matrix-data.frame-method | 1.626 | 0.159 | 1.433 | |
get_net_cls_tab | 1.801 | 0.217 | 1.667 | |
get_r2-mat | 0.874 | 0.029 | 0.562 | |
get_r2 | 0.885 | 0.033 | 0.579 | |
get_rep-matrix | 0.342 | 0.048 | 0.390 | |
get_rep-mima | 0.846 | 0.122 | 0.968 | |
hmp_des | 0.001 | 0.002 | 0.003 | |
hmp_otu | 0.001 | 0.001 | 0.001 | |
maize_asv | 0.001 | 0.001 | 0.002 | |
maize_asv2 | 0.001 | 0.001 | 0.002 | |
maize_des | 0.000 | 0.001 | 0.002 | |
maize_des2 | 0.000 | 0.002 | 0.002 | |
mina-class | 0.001 | 0.000 | 0.001 | |
net_cls-matrix | 16.658 | 0.870 | 17.195 | |
net_cls-mina | 19.089 | 1.005 | 19.743 | |
net_cls | 16.664 | 0.498 | 16.838 | |
net_cls_tab-mina-method | 3.253 | 0.150 | 3.105 | |
net_cls_tab | 1.893 | 0.309 | 1.872 | |
net_dis-mina | 18.936 | 4.651 | 21.976 | |
net_dis | 2.127 | 0.328 | 2.270 | |
net_dis_indi | 0.000 | 0.000 | 0.001 | |
net_dis_pcoa | 0 | 0 | 0 | |
net_dis_plot | 38.226 | 9.726 | 44.714 | |
net_grp_cmp | 0 | 0 | 0 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.042 | 0.050 | 0.093 | |
norm_tab-matrix | 0.853 | 0.043 | 0.897 | |
norm_tab-mina | 0.846 | 0.087 | 0.960 | |
norm_tab | 0.035 | 0.007 | 0.042 | |
norm_tab_method_list | 0.061 | 0.031 | 0.099 | |
pcoa_plot | 1.685 | 0.040 | 1.043 | |
sim_par | 0.000 | 0.001 | 0.001 | |
sparcc | 0.000 | 0.000 | 0.001 | |
tab_accessor | 0.000 | 0.000 | 0.001 | |
tina-matrix-method | 0.000 | 0.001 | 0.000 | |
tina | 0 | 0 | 0 | |