Rui Guan
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/mina |
| git_branch: devel |
| git_last_commit: fbaeda0 |
| git_last_commit_date: 2023-10-24 11:28:18 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:58 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 1256/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.11.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: mina |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings mina_1.11.0.tar.gz |
| StartedAt: 2024-03-28 07:17:08 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 07:22:44 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 336.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings mina_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mina.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘mina/DESCRIPTION’ ... OK
* this is package ‘mina’ version ‘1.11.0’
* 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 code 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 ... NOTE
checkRd: (-1) re_format_AP.Rd:10: Lost braces; missing escapes or markup?
10 | \item{x}{an {APResult} object from \pkg{apcluster}.}
| ^
* 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 94.080 1.323 90.426
net_dis-mina 47.847 1.078 45.875
dis_stat_accessor 34.915 0.563 33.626
com_plot-mina 21.156 0.041 3.510
bs_pm-mina 10.276 0.860 9.014
net_cls-mina 9.945 0.047 9.345
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/mina.Rcheck/00check.log’
for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 | 1.090 | 0.127 | 0.503 | |
| adj-mina | 1.567 | 0.008 | 0.929 | |
| adj | 1.284 | 0.000 | 0.643 | |
| adj_method_list | 0.080 | 0.005 | 0.097 | |
| bs_pm-mina | 10.276 | 0.860 | 9.014 | |
| bs_pm | 2.251 | 0.211 | 2.229 | |
| check_mina | 0.124 | 0.008 | 0.131 | |
| check_mina_de | 0.129 | 0.000 | 0.129 | |
| check_mina_qu | 0.125 | 0.004 | 0.129 | |
| cls_tab | 0.136 | 0.000 | 0.135 | |
| com_dis-matrix | 0.713 | 0.001 | 0.417 | |
| com_dis-mina | 0.410 | 0.019 | 0.142 | |
| com_dis | 0.670 | 0.004 | 0.402 | |
| com_dis_list | 0.113 | 0.007 | 0.121 | |
| com_plot-mina | 21.156 | 0.041 | 3.510 | |
| com_plot | 0.228 | 0.000 | 0.221 | |
| com_r2-mina | 1.017 | 0.012 | 0.705 | |
| com_r2 | 2.068 | 0.008 | 1.385 | |
| data-hmp | 0.001 | 0.000 | 0.002 | |
| data-maize | 0.001 | 0.000 | 0.000 | |
| des_accessor | 0.003 | 0.000 | 0.003 | |
| dis_accessor | 0.386 | 0.004 | 0.093 | |
| dis_stat_accessor | 34.915 | 0.563 | 33.626 | |
| dmr-matrix | 0.791 | 0.045 | 0.524 | |
| dmr-mina | 0.793 | 0.007 | 0.485 | |
| dmr | 0.744 | 0.016 | 0.494 | |
| dmr_accessor | 0.768 | 0.013 | 0.497 | |
| fit_tabs-mina | 1.470 | 0.052 | 1.525 | |
| fit_tabs | 2.374 | 0.067 | 2.448 | |
| get_net_cls_tab-matrix-data.frame-method | 2.873 | 0.021 | 2.234 | |
| get_net_cls_tab | 3.080 | 0.020 | 2.465 | |
| get_r2-mat | 0.970 | 0.016 | 0.680 | |
| get_r2 | 0.972 | 0.016 | 0.724 | |
| get_rep-matrix | 0.701 | 0.000 | 0.703 | |
| get_rep-mima | 1.660 | 0.008 | 1.672 | |
| 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 | 0.000 | |
| mina-class | 0.002 | 0.000 | 0.001 | |
| net_cls-matrix | 3.930 | 0.011 | 3.289 | |
| net_cls-mina | 9.945 | 0.047 | 9.345 | |
| net_cls | 4.007 | 0.024 | 3.427 | |
| net_cls_tab-mina-method | 3.236 | 0.020 | 2.603 | |
| net_cls_tab | 2.788 | 0.017 | 2.165 | |
| net_dis-mina | 47.847 | 1.078 | 45.875 | |
| net_dis | 2.333 | 0.152 | 2.299 | |
| net_dis_indi | 0 | 0 | 0 | |
| net_dis_pcoa | 0 | 0 | 0 | |
| net_dis_plot | 94.080 | 1.323 | 90.426 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0 | 0 | 0 | |
| norm_accessor | 0.055 | 0.000 | 0.055 | |
| norm_tab-matrix | 1.098 | 0.004 | 1.103 | |
| norm_tab-mina | 1.099 | 0.004 | 1.105 | |
| norm_tab | 0.054 | 0.000 | 0.054 | |
| norm_tab_method_list | 0.059 | 0.012 | 0.070 | |
| pcoa_plot | 1.692 | 0.008 | 1.059 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0 | 0 | 0 | |
| tab_accessor | 0.001 | 0.000 | 0.001 | |
| tina-matrix-method | 0 | 0 | 0 | |
| tina | 0 | 0 | 0 | |