| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:35 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 1211/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.9.0 (landing page) Rui Guan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: mina |
| Version: 1.9.0 |
| 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/site-library --timings mina_1.9.0.tar.gz |
| StartedAt: 2023-05-09 21:23:57 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 21:42:27 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 1109.4 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/site-library --timings mina_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mina.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 9.1Mb
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 89.912 2.016 85.577
net_cls-mina 47.979 0.201 47.487
net_dis-mina 45.256 1.335 43.259
net_cls 44.279 0.139 43.753
com_plot-mina 36.633 0.227 4.209
net_cls-matrix 36.413 0.074 35.823
dis_stat_accessor 33.928 0.944 32.494
bs_pm-mina 9.827 0.886 7.879
net_cls_tab-mina-method 6.442 0.068 5.840
* 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-devel_2023-03-12_r83975-bin/site-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++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -c cp_cor.cpp -o cp_cor.o g++ -std=gnu++17 -shared -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 | 1.113 | 0.146 | 0.451 | |
| adj-mina | 1.531 | 0.014 | 0.891 | |
| adj | 1.499 | 0.004 | 0.831 | |
| adj_method_list | 0.074 | 0.016 | 0.115 | |
| bs_pm-mina | 9.827 | 0.886 | 7.879 | |
| bs_pm | 2.172 | 0.411 | 2.191 | |
| check_mina | 0.138 | 0.004 | 0.141 | |
| check_mina_de | 0.134 | 0.003 | 0.138 | |
| check_mina_qu | 0.129 | 0.012 | 0.140 | |
| cls_tab | 0.139 | 0.004 | 0.142 | |
| com_dis-matrix | 0.731 | 0.003 | 0.374 | |
| com_dis-mina | 0.480 | 0.003 | 0.126 | |
| com_dis | 0.752 | 0.000 | 0.388 | |
| com_dis_list | 0.105 | 0.009 | 0.112 | |
| com_plot-mina | 36.633 | 0.227 | 4.209 | |
| com_plot | 0.232 | 0.008 | 0.232 | |
| com_r2-mina | 1.015 | 0.025 | 0.665 | |
| com_r2 | 2.446 | 0.046 | 1.574 | |
| data-hmp | 0.002 | 0.000 | 0.002 | |
| data-maize | 0.001 | 0.000 | 0.001 | |
| des_accessor | 0.003 | 0.000 | 0.003 | |
| dis_accessor | 0.433 | 0.000 | 0.079 | |
| dis_stat_accessor | 33.928 | 0.944 | 32.494 | |
| dmr-matrix | 0.847 | 0.021 | 0.510 | |
| dmr-mina | 0.831 | 0.016 | 0.483 | |
| dmr | 0.837 | 0.024 | 0.498 | |
| dmr_accessor | 0.825 | 0.015 | 0.479 | |
| fit_tabs-mina | 1.529 | 0.043 | 1.572 | |
| fit_tabs | 1.989 | 0.012 | 2.001 | |
| get_net_cls_tab-matrix-data.frame-method | 2.749 | 0.021 | 2.102 | |
| get_net_cls_tab | 2.934 | 0.001 | 2.259 | |
| get_r2-mat | 0.993 | 0.012 | 0.644 | |
| get_r2 | 0.949 | 0.003 | 0.600 | |
| get_rep-matrix | 0.719 | 0.012 | 0.730 | |
| get_rep-mima | 1.457 | 0.036 | 1.493 | |
| 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 | 0.001 | 0.000 | 0.001 | |
| mina-class | 0.001 | 0.000 | 0.001 | |
| net_cls-matrix | 36.413 | 0.074 | 35.823 | |
| net_cls-mina | 47.979 | 0.201 | 47.487 | |
| net_cls | 44.279 | 0.139 | 43.753 | |
| net_cls_tab-mina-method | 6.442 | 0.068 | 5.840 | |
| net_cls_tab | 2.538 | 0.013 | 1.872 | |
| net_dis-mina | 45.256 | 1.335 | 43.259 | |
| net_dis | 2.165 | 0.319 | 2.194 | |
| net_dis_indi | 0 | 0 | 0 | |
| net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
| net_dis_plot | 89.912 | 2.016 | 85.577 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0 | 0 | 0 | |
| norm_accessor | 0.047 | 0.004 | 0.051 | |
| norm_tab-matrix | 1.030 | 0.028 | 1.058 | |
| norm_tab-mina | 0.990 | 0.004 | 0.994 | |
| norm_tab | 0.049 | 0.000 | 0.049 | |
| norm_tab_method_list | 0.062 | 0.000 | 0.063 | |
| pcoa_plot | 1.816 | 0.009 | 1.096 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0 | 0 | 0 | |
| tab_accessor | 0.001 | 0.000 | 0.000 | |
| tina-matrix-method | 0.001 | 0.000 | 0.000 | |
| tina | 0.000 | 0.000 | 0.001 | |