Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:56 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 1259/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.10.0 (landing page) Rui Guan
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.10.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings mina_1.10.0.tar.gz |
StartedAt: 2023-11-02 12:10:52 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 12:13:37 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 164.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: mina.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:mina.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings mina_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mina.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * 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 ‘1.10.0’ * 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 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 7.2 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 ... ERROR Running examples in ‘mina-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dis_bs > ### Title: Getter for the slots 'dis_bs', 'dis_pm' and 'dis_stat'. > ### Aliases: dis_bs dis_pm dis_stat > > ### ** Examples > > maize <- new("mina", tab = maize_asv2, des = maize_des2) > maize <- norm_tab(maize, method = "raref") > maize <- fit_tabs(maize) > maize <- bs_pm(maize, group = "Compartment", per = 0.5) 1219 components are used for bs_pm before filtering. 313 samples are used for bs_pm before filtering. 2 groups with 276 samples used for bootstrap. > maize <- net_dis(maize, method = "Jaccard") * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 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-4.3.1/bin/R CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/lib -L/usr/local/lib -o mina.so RcppExports.o cp_cor.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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 | 1.116 | 0.024 | 0.468 | |
adj-mina | 1.331 | 0.012 | 0.675 | |
adj | 1.757 | 0.012 | 1.090 | |
adj_method_list | 0.078 | 0.024 | 0.170 | |
bs_pm-mina | 10.108 | 0.887 | 8.668 | |
bs_pm | 2.332 | 0.167 | 2.229 | |
check_mina | 0.115 | 0.016 | 0.132 | |
check_mina_de | 0.119 | 0.008 | 0.127 | |
check_mina_qu | 0.115 | 0.008 | 0.123 | |
cls_tab | 0.129 | 0.004 | 0.133 | |
com_dis-matrix | 0.757 | 0.004 | 0.412 | |
com_dis-mina | 0.469 | 0.002 | 0.139 | |
com_dis | 0.730 | 0.001 | 0.396 | |
com_dis_list | 0.111 | 0.006 | 0.117 | |
com_plot-mina | 36.185 | 0.648 | 4.383 | |
com_plot | 0.247 | 0.004 | 0.243 | |
com_r2-mina | 1.034 | 0.013 | 0.688 | |
com_r2 | 2.373 | 0.028 | 1.554 | |
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 | 0.422 | 0.004 | 0.083 | |