| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:38 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 1222/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.7.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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/site-library --timings mina_1.7.0.tar.gz |
| StartedAt: 2023-04-12 07:29:23 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 07:35:14 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 351.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mina.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking installed package size ... NOTE
installed size is 10.9Mb
sub-directories of 1Mb or more:
data 7.4Mb
libs 3.0Mb
* 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 42.744 4.282 31.128
net_dis-mina 21.756 3.377 16.352
dis_stat_accessor 17.103 2.431 13.415
com_plot-mina 14.707 0.117 1.529
bs_pm-mina 11.317 2.066 6.387
net_cls-mina 9.775 0.062 9.421
net_cls-matrix 6.588 0.156 6.324
net_cls 6.514 0.041 6.164
* 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/site-library’ * installing *source* package ‘mina’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c cp_cor.cpp -o cp_cor.o g++ -std=gnu++17 -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/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 | 0.653 | 0.053 | 0.316 | |
| adj-mina | 0.802 | 0.040 | 0.433 | |
| adj | 1.228 | 0.028 | 0.863 | |
| adj_method_list | 0.061 | 0.004 | 0.074 | |
| bs_pm-mina | 11.317 | 2.066 | 6.387 | |
| bs_pm | 2.822 | 0.229 | 1.790 | |
| check_mina | 0.071 | 0.016 | 0.088 | |
| check_mina_de | 0.064 | 0.017 | 0.081 | |
| check_mina_qu | 0.079 | 0.000 | 0.079 | |
| cls_tab | 0.077 | 0.003 | 0.080 | |
| com_dis-matrix | 0.630 | 0.000 | 0.267 | |
| com_dis-mina | 0.411 | 0.000 | 0.059 | |
| com_dis | 0.618 | 0.000 | 0.262 | |
| com_dis_list | 0.087 | 0.004 | 0.092 | |
| com_plot-mina | 14.707 | 0.117 | 1.529 | |
| com_plot | 0.174 | 0.010 | 0.164 | |
| com_r2-mina | 0.875 | 0.004 | 0.529 | |
| com_r2 | 1.299 | 0.032 | 0.950 | |
| 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 | 0.412 | 0.005 | 0.055 | |
| dis_stat_accessor | 17.103 | 2.431 | 13.415 | |
| dmr-matrix | 0.729 | 0.020 | 0.390 | |
| dmr-mina | 0.700 | 0.031 | 0.370 | |
| dmr | 0.683 | 0.000 | 0.335 | |
| dmr_accessor | 0.692 | 0.032 | 0.351 | |
| fit_tabs-mina | 0.599 | 0.176 | 0.775 | |
| fit_tabs | 1.171 | 0.096 | 1.268 | |
| get_net_cls_tab-matrix-data.frame-method | 1.493 | 0.082 | 1.177 | |
| get_net_cls_tab | 1.652 | 0.007 | 1.240 | |
| get_r2-mat | 0.774 | 0.000 | 0.432 | |
| get_r2 | 0.786 | 0.000 | 0.424 | |
| get_rep-matrix | 0.331 | 0.008 | 0.339 | |
| get_rep-mima | 0.670 | 0.023 | 0.693 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| maize_des | 0.000 | 0.000 | 0.001 | |
| maize_des2 | 0.000 | 0.000 | 0.001 | |
| mina-class | 0.000 | 0.000 | 0.001 | |
| net_cls-matrix | 6.588 | 0.156 | 6.324 | |
| net_cls-mina | 9.775 | 0.062 | 9.421 | |
| net_cls | 6.514 | 0.041 | 6.164 | |
| net_cls_tab-mina-method | 1.761 | 0.006 | 1.369 | |
| net_cls_tab | 1.446 | 0.052 | 1.096 | |
| net_dis-mina | 21.756 | 3.377 | 16.352 | |
| net_dis | 2.985 | 0.487 | 1.856 | |
| net_dis_indi | 0.001 | 0.000 | 0.001 | |
| net_dis_pcoa | 0 | 0 | 0 | |
| net_dis_plot | 42.744 | 4.282 | 31.128 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0 | 0 | 0 | |
| norm_accessor | 0.024 | 0.004 | 0.027 | |
| norm_tab-matrix | 0.772 | 0.027 | 0.798 | |
| norm_tab-mina | 0.758 | 0.003 | 0.761 | |
| norm_tab | 0.026 | 0.000 | 0.025 | |
| norm_tab_method_list | 0.051 | 0.008 | 0.058 | |
| pcoa_plot | 1.557 | 0.005 | 0.875 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0 | 0 | 0 | |
| tab_accessor | 0.000 | 0.000 | 0.001 | |
| tina-matrix-method | 0.001 | 0.000 | 0.000 | |
| tina | 0 | 0 | 0 | |