Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:39:32 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
kjohnson3 | macOS 13.6.5 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: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2024-05-03 23:13:28 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 23:17:35 -0400 (Fri, 03 May 2024) |
EllapsedTime: 246.6 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mina.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * 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 ‘1.12.0’ * 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: ‘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 35.458 38.556 37.387 net_dis-mina 18.380 19.472 19.491 dis_stat_accessor 14.483 17.327 14.958 bs_pm-mina 8.983 14.036 7.531 com_plot-mina 12.191 3.060 1.931 net_cls-mina 11.445 0.639 11.732 net_cls-matrix 7.010 0.551 7.133 net_cls 6.851 0.502 6.930 bs_pm 2.127 3.055 2.145 * 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-3.19-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 | 0.654 | 0.121 | 0.410 | |
adj-mina | 1.013 | 0.180 | 0.773 | |
adj | 0.755 | 0.172 | 0.500 | |
adj_method_list | 0.065 | 0.138 | 0.138 | |
bs_pm-mina | 8.983 | 14.036 | 7.531 | |
bs_pm | 2.127 | 3.055 | 2.145 | |
check_mina | 0.068 | 0.025 | 0.093 | |
check_mina_de | 0.065 | 0.021 | 0.087 | |
check_mina_qu | 0.065 | 0.021 | 0.088 | |
cls_tab | 0.072 | 0.052 | 0.127 | |
com_dis-matrix | 0.530 | 0.053 | 0.304 | |
com_dis-mina | 0.309 | 0.166 | 0.076 | |
com_dis | 0.527 | 0.183 | 0.303 | |
com_dis_list | 0.121 | 0.144 | 0.182 | |
com_plot-mina | 12.191 | 3.060 | 1.931 | |
com_plot | 0.180 | 0.195 | 0.185 | |
com_r2-mina | 0.778 | 0.209 | 0.561 | |
com_r2 | 1.248 | 0.385 | 1.009 | |
data-hmp | 0.001 | 0.001 | 0.002 | |
data-maize | 0.001 | 0.001 | 0.002 | |
des_accessor | 0.003 | 0.000 | 0.003 | |
dis_accessor | 0.288 | 0.053 | 0.056 | |
dis_stat_accessor | 14.483 | 17.327 | 14.958 | |
dmr-matrix | 0.596 | 0.213 | 0.374 | |
dmr-mina | 0.586 | 0.217 | 0.356 | |
dmr | 0.598 | 0.265 | 0.455 | |
dmr_accessor | 0.584 | 0.189 | 0.353 | |
fit_tabs-mina | 0.705 | 0.242 | 0.958 | |
fit_tabs | 1.186 | 0.345 | 1.553 | |
get_net_cls_tab-matrix-data.frame-method | 1.752 | 0.334 | 1.674 | |
get_net_cls_tab | 1.956 | 0.326 | 1.900 | |
get_r2-mat | 0.744 | 0.171 | 0.530 | |
get_r2 | 0.770 | 0.214 | 0.620 | |
get_rep-matrix | 0.285 | 0.012 | 0.301 | |
get_rep-mima | 0.737 | 0.066 | 0.809 | |
hmp_des | 0.001 | 0.001 | 0.002 | |
hmp_otu | 0.001 | 0.001 | 0.002 | |
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 | 0.001 | 0.001 | 0.003 | |
mina-class | 0.001 | 0.001 | 0.001 | |
net_cls-matrix | 7.010 | 0.551 | 7.133 | |
net_cls-mina | 11.445 | 0.639 | 11.732 | |
net_cls | 6.851 | 0.502 | 6.930 | |
net_cls_tab-mina-method | 1.919 | 0.119 | 1.652 | |
net_cls_tab | 1.703 | 0.323 | 1.599 | |
net_dis-mina | 18.380 | 19.472 | 19.491 | |
net_dis | 2.008 | 2.723 | 2.215 | |
net_dis_indi | 0.000 | 0.001 | 0.001 | |
net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
net_dis_plot | 35.458 | 38.556 | 37.387 | |
net_grp_cmp | 0.000 | 0.000 | 0.001 | |
net_node_cmp | 0 | 0 | 0 | |
norm_accessor | 0.031 | 0.001 | 0.031 | |
norm_tab-matrix | 0.882 | 0.014 | 0.908 | |
norm_tab-mina | 0.781 | 0.078 | 0.871 | |
norm_tab | 0.03 | 0.00 | 0.03 | |
norm_tab_method_list | 0.069 | 0.043 | 0.133 | |
pcoa_plot | 1.258 | 0.522 | 0.844 | |
sim_par | 0.000 | 0.000 | 0.001 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0.001 | 0.001 | 0.001 | |
tina-matrix-method | 0.000 | 0.001 | 0.001 | |
tina | 0.000 | 0.001 | 0.001 | |