| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:38 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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 1213/2197 | 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/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: 2023-05-30 12:12:14 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 12:26:09 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 835.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
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### Running 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
###
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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 (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 11.3.0-1ubuntu1~22.04.1) 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 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 7.4 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 96.774 3.044 93.242
net_cls-mina 62.363 0.268 61.944
net_dis-mina 49.165 1.040 47.174
net_cls 43.495 0.082 42.890
com_plot-mina 36.455 0.161 4.024
net_cls-matrix 35.681 0.089 35.089
dis_stat_accessor 33.319 0.940 31.887
bs_pm-mina 10.155 0.623 8.416
net_cls_tab-mina-method 6.520 0.035 5.869
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ 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/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/site-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/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/site-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 | 1.102 | 0.138 | 0.445 | |
| adj-mina | 1.270 | 0.029 | 0.635 | |
| adj | 1.707 | 0.013 | 1.048 | |
| adj_method_list | 0.065 | 0.020 | 0.099 | |
| bs_pm-mina | 10.155 | 0.623 | 8.416 | |
| bs_pm | 2.155 | 0.409 | 2.147 | |
| check_mina | 0.132 | 0.008 | 0.141 | |
| check_mina_de | 0.136 | 0.001 | 0.137 | |
| check_mina_qu | 0.134 | 0.004 | 0.138 | |
| cls_tab | 0.141 | 0.000 | 0.141 | |
| com_dis-matrix | 0.746 | 0.007 | 0.387 | |
| com_dis-mina | 0.478 | 0.007 | 0.129 | |
| com_dis | 0.714 | 0.019 | 0.374 | |
| com_dis_list | 0.116 | 0.002 | 0.118 | |
| com_plot-mina | 36.455 | 0.161 | 4.024 | |
| com_plot | 0.237 | 0.004 | 0.232 | |
| com_r2-mina | 0.991 | 0.029 | 0.669 | |
| com_r2 | 2.397 | 0.045 | 1.538 | |
| data-hmp | 0.000 | 0.001 | 0.001 | |
| data-maize | 0.000 | 0.001 | 0.001 | |
| des_accessor | 0.002 | 0.000 | 0.003 | |
| dis_accessor | 0.444 | 0.003 | 0.094 | |
| dis_stat_accessor | 33.319 | 0.940 | 31.887 | |
| dmr-matrix | 0.863 | 0.013 | 0.518 | |
| dmr-mina | 0.864 | 0.007 | 0.496 | |
| dmr | 0.821 | 0.033 | 0.487 | |
| dmr_accessor | 0.834 | 0.004 | 0.483 | |
| fit_tabs-mina | 1.439 | 0.063 | 1.502 | |
| fit_tabs | 1.959 | 0.104 | 2.063 | |
| get_net_cls_tab-matrix-data.frame-method | 2.585 | 0.017 | 1.930 | |
| get_net_cls_tab | 2.776 | 0.005 | 2.092 | |
| get_r2-mat | 0.964 | 0.008 | 0.620 | |
| get_r2 | 0.957 | 0.005 | 0.602 | |
| get_rep-matrix | 0.703 | 0.012 | 0.715 | |
| get_rep-mima | 1.509 | 0.012 | 1.520 | |
| hmp_des | 0.001 | 0.000 | 0.001 | |
| hmp_otu | 0.001 | 0.000 | 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 | 35.681 | 0.089 | 35.089 | |
| net_cls-mina | 62.363 | 0.268 | 61.944 | |
| net_cls | 43.495 | 0.082 | 42.890 | |
| net_cls_tab-mina-method | 6.520 | 0.035 | 5.869 | |
| net_cls_tab | 2.718 | 0.048 | 2.104 | |
| net_dis-mina | 49.165 | 1.040 | 47.174 | |
| net_dis | 2.225 | 0.233 | 2.162 | |
| net_dis_indi | 0 | 0 | 0 | |
| net_dis_pcoa | 0.000 | 0.000 | 0.001 | |
| net_dis_plot | 96.774 | 3.044 | 93.242 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0 | 0 | 0 | |
| norm_accessor | 0.053 | 0.000 | 0.053 | |
| norm_tab-matrix | 1.056 | 0.024 | 1.080 | |
| norm_tab-mina | 1.039 | 0.016 | 1.055 | |
| norm_tab | 0.053 | 0.000 | 0.053 | |
| norm_tab_method_list | 0.062 | 0.012 | 0.074 | |
| pcoa_plot | 1.850 | 0.005 | 1.127 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0 | 0 | 0 | |
| tab_accessor | 0.000 | 0.000 | 0.001 | |
| tina-matrix-method | 0.000 | 0.000 | 0.001 | |
| tina | 0 | 0 | 0 | |