Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-01-23 12:12 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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 1263/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.14.0  (landing page)
Rui Guan
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/mina
git_branch: RELEASE_3_20
git_last_commit: f80a036
git_last_commit_date: 2024-10-29 10:53:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for mina on taishan

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.

raw results


Summary

Package: mina
Version: 1.14.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data mina
StartedAt: 2025-01-21 01:13:23 -0000 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 01:14:11 -0000 (Tue, 21 Jan 2025)
EllapsedTime: 48.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data mina
###
##############################################################################
##############################################################################


* checking for file ‘mina/DESCRIPTION’ ... OK
* preparing ‘mina’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘mina.Rmd’ using rmarkdown
norm_tab_method_list           package:mina            R Documentation

_L_i_s_t _o_f _n_o_r_m_a_l_i_z_a_t_i_o_n _m_e_t_h_o_d_s _s_u_p_p_o_r_t_e_d _i_n '_n_o_r_m__t_a_b'

_D_e_s_c_r_i_p_t_i_o_n:

     Normalization methods should be specified by exact string match.

_U_s_a_g_e:

     norm_tab_method_list
     
_F_o_r_m_a_t:

     A list of character vectors.

     'raref' By downsampling all samples to specific depth.

     'total' Devided by the total read of each sample.

_S_e_e _A_l_s_o:

     'norm_tab'

_E_x_a_m_p_l_e_s:

     ? norm_tab_method_list
     

com_dis_list               package:mina                R Documentation

_L_i_s_t _o_f _d_i_s_s_i_m_i_l_a_r_i_t_y / _d_i_s_t_a_n_c_e _s_u_p_p_o_r_t_e_d _i_n '_c_o_m__d_i_s'. _D_i_s_s_i_m_i_l_a_r_i_t_y
/ _d_i_s_t_a_n_c_e _s_h_o_u_l_d _b_e _s_p_e_c_i_f_i_e_d _b_y _e_x_a_c_t _s_t_r_i_n_g _m_a_t_c_h.

_D_e_s_c_r_i_p_t_i_o_n:

     List of dissimilarity / distance supported in 'com_dis'.
     Dissimilarity / distance should be specified by exact string
     match.

_U_s_a_g_e:

     com_dis_list
     
_F_o_r_m_a_t:

     A list of character vectors indicate the dissimilarity / distance
     method used.

     'tina' TINA from Schmidt_et_al_2016

     'Jaccard' Jaccard defined by 'vegdist'

     weighted Dissimilarity / distance method for weighted matrix:

     'bhjattacharyya' from 'parDist'

     'canberra' from 'parDist'

     'bray' from 'parDist'

     'chord' from 'parDist'

     'divergence' from 'parDist'

     'euclidean' from 'parDist'

     'fJaccard' from 'parDist'

     'geodesic' from 'parDist'

     'hellinger' from 'parDist'

     'kullback' from 'parDist'

     'manhattan' from 'parDist'

     'maximum' from 'parDist'

     'minkowski' from 'parDist'

     'podani' from 'parDist'

     'soergel' from 'parDist'

     'wave' from 'parDist'

     'whittaker' from 'parDist'

     unweighted Dissimilarity / Distance for unweighted matrix:

     'binary' from 'parDist'

     'braun-blanquet' from 'parDist'

     'consine' from 'parDist'

     'dice' from 'parDist'

     'fager' from 'parDist'

     'faith' from 'parDist'

     'hamman' from 'parDist'

     'hamming' from 'parDist'

     'kulczynski1' from 'parDist'

     'kulczynski2' from 'parDist'

     'michael' from 'parDist'

     'mountford' from 'parDist'

     'mozley' from 'parDist'

     'ochiai' from 'parDist'

     'phi' from 'parDist'

     'russel' from 'parDist'

     'simple matching' from 'parDist'

     'simpson' from 'parDist'

     'stiles' from 'parDist'

     'tanimoto' from 'parDist'

     'yule' from 'parDist'

     'yule2' from 'parDist'

_E_x_a_m_p_l_e_s:

     ? com_dis_list
     


 *** caught segfault ***
address 0x211000002, cause 'memory not mapped'

 *** caught bus error ***
address 0x3431006109, cause 'invalid alignment'