Rui Guan
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/mina |
| git_branch: RELEASE_3_17 |
| git_last_commit: 41f0451 |
| git_last_commit_date: 2023-04-25 11:25:14 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1232/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.8.0 (landing page) Rui Guan
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the mina package: - 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2023-10-18 07:41:16 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 07:48:22 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 425.5 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mina.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mina/DESCRIPTION’ ... OK
* this is package ‘mina’ version ‘1.8.0’
* 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 31.561 7.542 59.469
net_cls-mina 18.930 0.772 28.620
net_dis-mina 15.768 3.443 29.100
net_cls 14.516 0.489 22.744
net_cls-matrix 14.613 0.349 21.549
dis_stat_accessor 12.644 1.976 21.830
com_plot-mina 12.063 0.272 18.867
bs_pm-mina 6.933 0.385 10.900
net_cls_tab-mina-method 3.538 0.142 5.245
* 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-3.17-bioc-mac-arm64/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-arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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 -single_module -multiply_defined suppress -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/4.3-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 | 0.714 | 0.032 | 0.855 | |
| adj-mina | 1.047 | 0.022 | 1.306 | |
| adj | 0.995 | 0.019 | 1.219 | |
| adj_method_list | 0.074 | 0.049 | 0.204 | |
| bs_pm-mina | 6.933 | 0.385 | 10.900 | |
| bs_pm | 1.731 | 0.092 | 2.776 | |
| check_mina | 0.064 | 0.016 | 0.122 | |
| check_mina_de | 0.062 | 0.015 | 0.125 | |
| check_mina_qu | 0.061 | 0.014 | 0.116 | |
| cls_tab | 0.069 | 0.019 | 0.138 | |
| com_dis-matrix | 0.832 | 0.027 | 1.282 | |
| com_dis-mina | 0.523 | 0.016 | 0.822 | |
| com_dis | 0.844 | 0.030 | 1.332 | |
| com_dis_list | 0.119 | 0.035 | 0.258 | |
| com_plot-mina | 12.063 | 0.272 | 18.867 | |
| com_plot | 0.190 | 0.006 | 0.306 | |
| com_r2-mina | 1.049 | 0.032 | 1.804 | |
| com_r2 | 1.602 | 0.148 | 1.649 | |
| data-hmp | 0.001 | 0.001 | 0.003 | |
| data-maize | 0.001 | 0.001 | 0.001 | |
| des_accessor | 0.003 | 0.000 | 0.004 | |
| dis_accessor | 0.426 | 0.008 | 0.290 | |
| dis_stat_accessor | 12.644 | 1.976 | 21.830 | |
| dmr-matrix | 0.811 | 0.060 | 0.864 | |
| dmr-mina | 0.808 | 0.014 | 0.843 | |
| dmr | 0.773 | 0.018 | 0.764 | |
| dmr_accessor | 0.758 | 0.032 | 0.806 | |
| fit_tabs-mina | 0.574 | 0.119 | 0.991 | |
| fit_tabs | 0.998 | 0.104 | 1.685 | |
| get_net_cls_tab-matrix-data.frame-method | 2.042 | 0.121 | 2.799 | |
| get_net_cls_tab | 2.227 | 0.144 | 2.961 | |
| get_r2-mat | 0.910 | 0.022 | 0.896 | |
| get_r2 | 0.993 | 0.049 | 1.024 | |
| get_rep-matrix | 0.246 | 0.017 | 0.334 | |
| get_rep-mima | 0.898 | 0.046 | 1.203 | |
| hmp_des | 0.001 | 0.001 | 0.002 | |
| hmp_otu | 0.001 | 0.001 | 0.003 | |
| maize_asv | 0.001 | 0.001 | 0.003 | |
| maize_asv2 | 0.001 | 0.001 | 0.005 | |
| 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 | 14.613 | 0.349 | 21.549 | |
| net_cls-mina | 18.930 | 0.772 | 28.620 | |
| net_cls | 14.516 | 0.489 | 22.744 | |
| net_cls_tab-mina-method | 3.538 | 0.142 | 5.245 | |
| net_cls_tab | 1.988 | 0.112 | 2.836 | |
| net_dis-mina | 15.768 | 3.443 | 29.100 | |
| net_dis | 1.752 | 0.129 | 2.824 | |
| net_dis_indi | 0.000 | 0.000 | 0.001 | |
| net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
| net_dis_plot | 31.561 | 7.542 | 59.469 | |
| net_grp_cmp | 0.001 | 0.000 | 0.000 | |
| net_node_cmp | 0.000 | 0.000 | 0.001 | |
| norm_accessor | 0.030 | 0.003 | 0.056 | |
| norm_tab-matrix | 1.023 | 0.073 | 1.738 | |
| norm_tab-mina | 1.004 | 0.129 | 1.719 | |
| norm_tab | 0.031 | 0.003 | 0.048 | |
| norm_tab_method_list | 0.070 | 0.044 | 0.191 | |
| pcoa_plot | 1.936 | 0.064 | 2.981 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0.000 | 0.000 | 0.001 | |
| tab_accessor | 0.001 | 0.000 | 0.001 | |
| tina-matrix-method | 0.000 | 0.000 | 0.001 | |
| tina | 0.000 | 0.001 | 0.000 | |