| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:36 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1215/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.9.0 (landing page) Rui Guan
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: mina |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings mina_1.9.0.tar.gz |
| StartedAt: 2023-06-06 02:06:25 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 02:24:20 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 1074.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings mina_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mina.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘mina/DESCRIPTION’ ... OK
* this is package ‘mina’ version ‘1.9.0’
* 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: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
data 7.2Mb
libs 1.5Mb
* 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 loading without being on the library search path ... 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 7.2 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 91.976 1.404 87.444
net_cls-mina 56.979 0.069 56.489
net_cls 49.492 0.252 49.151
net_cls-matrix 48.029 0.132 47.578
net_dis-mina 46.668 0.749 44.323
dis_stat_accessor 34.678 0.573 33.147
com_plot-mina 21.827 0.121 3.553
bs_pm-mina 9.770 0.811 8.318
net_cls_tab-mina-method 7.114 0.028 6.502
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘mina.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/mina.Rcheck/00check.log’
for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -c cp_cor.cpp -o cp_cor.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-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 | 1.123 | 0.110 | 0.452 | |
| adj-mina | 1.507 | 0.004 | 0.877 | |
| adj | 1.469 | 0.042 | 0.841 | |
| adj_method_list | 0.070 | 0.070 | 0.157 | |
| bs_pm-mina | 9.770 | 0.811 | 8.318 | |
| bs_pm | 2.270 | 0.142 | 2.201 | |
| check_mina | 0.128 | 0.008 | 0.136 | |
| check_mina_de | 0.124 | 0.000 | 0.124 | |
| check_mina_qu | 0.120 | 0.004 | 0.124 | |
| cls_tab | 0.127 | 0.004 | 0.131 | |
| com_dis-matrix | 0.684 | 0.010 | 0.388 | |
| com_dis-mina | 0.411 | 0.006 | 0.123 | |
| com_dis | 0.672 | 0.005 | 0.385 | |
| com_dis_list | 0.098 | 0.013 | 0.111 | |
| com_plot-mina | 21.827 | 0.121 | 3.553 | |
| com_plot | 0.238 | 0.000 | 0.230 | |
| com_r2-mina | 0.971 | 0.011 | 0.687 | |
| com_r2 | 2.379 | 0.052 | 1.584 | |
| data-hmp | 0.000 | 0.001 | 0.002 | |
| data-maize | 0.000 | 0.001 | 0.001 | |
| des_accessor | 0.002 | 0.001 | 0.003 | |
| dis_accessor | 0.427 | 0.000 | 0.084 | |
| dis_stat_accessor | 34.678 | 0.573 | 33.147 | |
| dmr-matrix | 0.773 | 0.032 | 0.533 | |
| dmr-mina | 0.852 | 0.012 | 0.516 | |
| dmr | 0.811 | 0.008 | 0.526 | |
| dmr_accessor | 0.787 | 0.004 | 0.515 | |
| fit_tabs-mina | 1.532 | 0.024 | 1.559 | |
| fit_tabs | 2.030 | 0.012 | 2.045 | |
| get_net_cls_tab-matrix-data.frame-method | 2.554 | 0.015 | 1.900 | |
| get_net_cls_tab | 2.822 | 0.009 | 2.157 | |
| get_r2-mat | 0.950 | 0.004 | 0.628 | |
| get_r2 | 0.912 | 0.001 | 0.596 | |
| get_rep-matrix | 0.715 | 0.000 | 0.717 | |
| get_rep-mima | 1.475 | 0.004 | 1.482 | |
| hmp_des | 0.001 | 0.000 | 0.001 | |
| hmp_otu | 0.000 | 0.000 | 0.001 | |
| maize_asv | 0.001 | 0.000 | 0.001 | |
| maize_asv2 | 0.001 | 0.000 | 0.001 | |
| maize_des | 0.000 | 0.000 | 0.001 | |
| maize_des2 | 0.001 | 0.000 | 0.001 | |
| mina-class | 0.001 | 0.000 | 0.001 | |
| net_cls-matrix | 48.029 | 0.132 | 47.578 | |
| net_cls-mina | 56.979 | 0.069 | 56.489 | |
| net_cls | 49.492 | 0.252 | 49.151 | |
| net_cls_tab-mina-method | 7.114 | 0.028 | 6.502 | |
| net_cls_tab | 2.540 | 0.039 | 1.915 | |
| net_dis-mina | 46.668 | 0.749 | 44.323 | |
| net_dis | 2.375 | 0.058 | 2.179 | |
| net_dis_indi | 0 | 0 | 0 | |
| net_dis_pcoa | 0 | 0 | 0 | |
| net_dis_plot | 91.976 | 1.404 | 87.444 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0.000 | 0.000 | 0.001 | |
| norm_accessor | 0.052 | 0.000 | 0.053 | |
| norm_tab-matrix | 1.056 | 0.012 | 1.070 | |
| norm_tab-mina | 1.013 | 0.000 | 1.015 | |
| norm_tab | 0.052 | 0.000 | 0.052 | |
| norm_tab_method_list | 0.059 | 0.003 | 0.061 | |
| pcoa_plot | 1.678 | 0.008 | 1.111 | |
| sim_par | 0.000 | 0.000 | 0.001 | |
| sparcc | 0 | 0 | 0 | |
| tab_accessor | 0.001 | 0.000 | 0.000 | |
| tina-matrix-method | 0.000 | 0.000 | 0.001 | |
| tina | 0 | 0 | 0 | |