| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:44 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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: - 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1194/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.7.0 (landing page) Rui Guan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: mina |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings mina_1.7.0.tar.gz |
| StartedAt: 2023-02-28 08:21:22 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 08:38:33 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 1031.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings mina_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mina.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mina/DESCRIPTION’ ... OK
* this is package ‘mina’ version ‘1.7.0’
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
data 7.4Mb
libs 1.2Mb
* 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 93.253 2.920 89.627
net_cls-mina 46.944 0.130 46.421
net_dis-mina 45.390 1.046 43.268
com_plot-mina 36.202 0.127 3.835
dis_stat_accessor 32.667 1.085 31.399
net_cls-matrix 32.001 0.106 31.438
net_cls 31.412 0.079 30.863
bs_pm-mina 9.872 0.908 8.475
net_cls_tab-mina-method 6.417 0.004 5.769
* 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-3.17-bioc/meat/mina.Rcheck/00check.log’
for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cp_cor.cpp -o cp_cor.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 | 1.095 | 0.064 | 0.436 | |
| adj-mina | 1.355 | 0.012 | 0.688 | |
| adj | 1.735 | 0.377 | 1.403 | |
| adj_method_list | 0.070 | 0.009 | 0.104 | |
| bs_pm-mina | 9.872 | 0.908 | 8.475 | |
| bs_pm | 2.297 | 0.367 | 2.185 | |
| check_mina | 0.139 | 0.005 | 0.144 | |
| check_mina_de | 0.132 | 0.008 | 0.140 | |
| check_mina_qu | 0.130 | 0.007 | 0.137 | |
| cls_tab | 0.140 | 0.000 | 0.141 | |
| com_dis-matrix | 0.711 | 0.007 | 0.362 | |
| com_dis-mina | 0.475 | 0.005 | 0.123 | |
| com_dis | 0.710 | 0.011 | 0.371 | |
| com_dis_list | 0.111 | 0.004 | 0.115 | |
| com_plot-mina | 36.202 | 0.127 | 3.835 | |
| com_plot | 0.243 | 0.001 | 0.235 | |
| com_r2-mina | 1.004 | 0.020 | 0.664 | |
| com_r2 | 2.406 | 0.072 | 1.523 | |
| data-hmp | 0.001 | 0.000 | 0.002 | |
| data-maize | 0.001 | 0.000 | 0.001 | |
| des_accessor | 0.004 | 0.000 | 0.003 | |
| dis_accessor | 0.442 | 0.004 | 0.092 | |
| dis_stat_accessor | 32.667 | 1.085 | 31.399 | |
| dmr-matrix | 0.830 | 0.016 | 0.489 | |
| dmr-mina | 0.825 | 0.016 | 0.489 | |
| dmr | 0.834 | 0.001 | 0.471 | |
| dmr_accessor | 0.868 | 0.000 | 0.500 | |
| fit_tabs-mina | 1.491 | 0.068 | 1.559 | |
| fit_tabs | 1.990 | 0.024 | 2.015 | |
| get_net_cls_tab-matrix-data.frame-method | 2.672 | 0.024 | 2.011 | |
| get_net_cls_tab | 2.748 | 0.035 | 2.113 | |
| get_r2-mat | 0.956 | 0.000 | 0.604 | |
| get_r2 | 0.994 | 0.003 | 0.632 | |
| get_rep-matrix | 0.748 | 0.008 | 0.756 | |
| get_rep-mima | 1.469 | 0.005 | 1.474 | |
| hmp_des | 0.000 | 0.001 | 0.001 | |
| hmp_otu | 0.000 | 0.001 | 0.001 | |
| maize_asv | 0.001 | 0.000 | 0.001 | |
| maize_asv2 | 0.001 | 0.000 | 0.001 | |
| maize_des | 0.001 | 0.000 | 0.001 | |
| maize_des2 | 0.000 | 0.000 | 0.001 | |
| mina-class | 0.001 | 0.000 | 0.001 | |
| net_cls-matrix | 32.001 | 0.106 | 31.438 | |
| net_cls-mina | 46.944 | 0.130 | 46.421 | |
| net_cls | 31.412 | 0.079 | 30.863 | |
| net_cls_tab-mina-method | 6.417 | 0.004 | 5.769 | |
| net_cls_tab | 2.531 | 0.021 | 1.900 | |
| net_dis-mina | 45.390 | 1.046 | 43.268 | |
| net_dis | 2.036 | 0.478 | 2.224 | |
| net_dis_indi | 0.000 | 0.000 | 0.001 | |
| net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
| net_dis_plot | 93.253 | 2.920 | 89.627 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0.000 | 0.000 | 0.001 | |
| norm_accessor | 0.043 | 0.012 | 0.054 | |
| norm_tab-matrix | 1.062 | 0.016 | 1.078 | |
| norm_tab-mina | 1.009 | 0.008 | 1.017 | |
| norm_tab | 0.049 | 0.000 | 0.050 | |
| norm_tab_method_list | 0.059 | 0.007 | 0.065 | |
| pcoa_plot | 1.793 | 0.022 | 1.091 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0.000 | 0.000 | 0.001 | |
| tab_accessor | 0 | 0 | 0 | |
| tina-matrix-method | 0 | 0 | 0 | |
| tina | 0.000 | 0.001 | 0.000 | |