Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the mina package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1137/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.0.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: mina |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mina.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mina_1.0.0.tar.gz |
StartedAt: 2021-10-14 21:09:09 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:13:12 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 242.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mina.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mina_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/mina.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mina/DESCRIPTION’ ... OK * this is package ‘mina’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’ * 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 * checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: data 8.0Mb * 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_indi,character-character: no visible binding for global variable ‘out_dir’ Undefined global functions or variables: i out_dir * 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-mina 20.999 6.355 21.580 com_plot-mina 20.978 0.188 2.812 dis_stat_accessor 15.881 4.162 15.903 net_cls-mina 15.585 0.667 15.960 net_dis 10.012 3.187 7.892 bs_pm-mina 9.659 3.081 8.195 bs_pm 8.175 2.783 6.744 net_cls 8.289 0.309 8.310 net_cls-matrix 8.217 0.245 8.174 * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/mina.Rcheck/00check.log’ for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cp_cor.cpp -o cp_cor.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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 | 0.702 | 0.074 | 0.487 | |
adj-mina | 0.876 | 0.095 | 0.664 | |
adj | 0.917 | 0.077 | 0.692 | |
adj_method_list | 0.079 | 0.034 | 0.137 | |
bs_pm-mina | 9.659 | 3.081 | 8.195 | |
bs_pm | 8.175 | 2.783 | 6.744 | |
check_mina | 0.138 | 0.026 | 0.166 | |
check_mina_de | 0.134 | 0.025 | 0.160 | |
check_mina_qu | 0.144 | 0.026 | 0.170 | |
cls_tab | 0.112 | 0.021 | 0.133 | |
com_dis-matrix | 1.589 | 0.016 | 0.482 | |
com_dis-mina | 1.386 | 0.021 | 0.131 | |
com_dis | 1.595 | 0.057 | 0.521 | |
com_dis_list | 0.111 | 0.021 | 0.133 | |
com_plot-mina | 20.978 | 0.188 | 2.812 | |
com_plot | 0.181 | 0.023 | 0.173 | |
com_r2-mina | 1.865 | 0.034 | 0.750 | |
com_r2 | 1.263 | 0.077 | 0.884 | |
data-hmp | 0.002 | 0.001 | 0.003 | |
data-maize | 0.001 | 0.001 | 0.003 | |
des_accessor | 0.005 | 0.001 | 0.006 | |
dis_accessor | 1.234 | 0.018 | 0.124 | |
dis_stat_accessor | 15.881 | 4.162 | 15.903 | |
dmr-matrix | 1.720 | 0.014 | 0.580 | |
dmr-mina | 1.889 | 0.112 | 0.659 | |
dmr | 1.815 | 0.019 | 0.485 | |
dmr_accessor | 1.666 | 0.029 | 0.533 | |
fit_tabs-mina | 0.863 | 0.166 | 1.031 | |
fit_tabs | 1.241 | 0.101 | 1.345 | |
get_net_cls_tab-matrix-data.frame-method | 2.379 | 0.195 | 2.263 | |
get_net_cls_tab | 2.544 | 0.255 | 2.509 | |
get_r2-mat | 1.760 | 0.020 | 0.626 | |
get_r2 | 1.944 | 0.077 | 0.712 | |
hmp_des | 0.001 | 0.001 | 0.002 | |
hmp_otu | 0.001 | 0.001 | 0.001 | |
maize_asv | 0.001 | 0.000 | 0.002 | |
maize_asv2 | 0.000 | 0.001 | 0.002 | |
maize_des | 0.001 | 0.001 | 0.002 | |
maize_des2 | 0.001 | 0.001 | 0.002 | |
mina-class | 0.001 | 0.000 | 0.001 | |
net_cls-matrix | 8.217 | 0.245 | 8.174 | |
net_cls-mina | 15.585 | 0.667 | 15.960 | |
net_cls | 8.289 | 0.309 | 8.310 | |
net_cls_tab-mina-method | 2.147 | 0.099 | 1.950 | |
net_cls_tab | 2.354 | 0.155 | 2.218 | |
net_dis-mina | 20.999 | 6.355 | 21.580 | |
net_dis | 10.012 | 3.187 | 7.892 | |
net_dis_indi | 0.000 | 0.001 | 0.001 | |
norm_accessor | 0.033 | 0.000 | 0.033 | |
norm_tab-matrix | 1.007 | 0.002 | 1.010 | |
norm_tab-mina | 1.141 | 0.103 | 1.245 | |
norm_tab | 0.043 | 0.000 | 0.043 | |
norm_tab_method_list | 0.073 | 0.024 | 0.100 | |
pcoa_plot | 3.565 | 0.044 | 1.203 | |
sim_par | 0.000 | 0.001 | 0.000 | |
sparcc | 0 | 0 | 0 | |
tab_accessor | 0.001 | 0.001 | 0.001 | |
tina-matrix-method | 0.000 | 0.000 | 0.001 | |
tina | 0.000 | 0.000 | 0.001 | |