Back to Multiple platform build/check report for BioC 3.20:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-11-20 12:01 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 58/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.8.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_20
git_last_commit: ab34115
git_last_commit_date: 2024-10-29 10:53:23 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped


CHECK results for AlpsNMR on teran2

To the developers/maintainers of the AlpsNMR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlpsNMR.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.

raw results


Summary

Package: AlpsNMR
Version: 4.8.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AlpsNMR_4.8.0.tar.gz
StartedAt: 2024-11-19 22:44:53 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 22:48:44 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 231.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AlpsNMR_4.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.8.0’
* 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 ‘AlpsNMR’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
Peak_detection                      6.726  2.039   6.368
SummarizedExperiment_to_nmr_data_1r 6.029  0.620   6.117
permutation_test_plot               4.134  2.248   1.425
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘AlpsNMR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AlpsNMR)

Tests output

AlpsNMR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(AlpsNMR)

Attaching package: 'AlpsNMR'

The following object is masked from 'package:stats':

    filter

> 
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_rDolphin.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]
> 
> proc.time()
   user  system elapsed 
 23.926   9.669  22.186 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.6100.4321.830
HMDB_blood0.0030.0010.005
HMDB_cell0.0010.0010.002
HMDB_urine0.0030.0000.003
Parameters_blood0.0010.0000.002
Parameters_cell0.0020.0000.001
Parameters_urine0.0010.0000.001
Peak_detection6.7262.0396.368
Pipelines0.0010.0000.001
ROI_blood0.0030.0000.002
ROI_cell0.0010.0020.002
ROI_urine0.0020.0000.002
SummarizedExperiment_to_nmr_data_1r6.0290.6206.117
SummarizedExperiment_to_nmr_dataset_peak_table0.7350.4820.672
bp_VIP_analysis0.8140.7590.746
bp_kfold_VIP_analysis0.8170.6640.444
download_MTBLS242000
file_lister0.0470.0150.061
files_to_rDolphin000
filter.nmr_dataset_family0.6710.5550.564
format.nmr_dataset2.9031.9162.182
format.nmr_dataset_1D0.5460.5300.493
format.nmr_dataset_peak_table0.6200.4760.510
get_integration_with_metadata0.0210.0020.024
hmdb0.0390.0020.042
is.nmr_dataset0.5270.4960.437
is.nmr_dataset_1D0.5410.5330.500
is.nmr_dataset_peak_table0.5660.4490.488
load_and_save_functions0.5370.4430.418
models_stability_plot_bootstrap0.0000.0000.001
models_stability_plot_plsda0.2570.4430.352
new_nmr_dataset0.0010.0000.001
new_nmr_dataset_1D0.0000.0000.001
new_nmr_dataset_peak_table0.6600.6160.570
nmr_autophase0.1390.0590.228
nmr_baseline_estimation0.0230.0430.009
nmr_baseline_removal0.0030.0000.004
nmr_baseline_threshold0.0010.0000.001
nmr_baseline_threshold_plot0.1490.0370.187
nmr_batman0.0030.0000.003
nmr_batman_options000
nmr_build_peak_table0.0170.0130.030
nmr_data0.0310.0100.040
nmr_data_1r_to_SummarizedExperiment0.7320.6020.689
nmr_data_analysis0.3200.5090.383
nmr_dataset0.0000.0000.001
nmr_dataset_1D0.0010.0000.001
nmr_dataset_peak_table_to_SummarizedExperiment0.7480.5310.650
nmr_exclude_region0.0030.0010.004
nmr_export_data_1r0.5610.4840.492
nmr_get_peak_distances0.0070.0000.007
nmr_identify_regions_blood0.0090.0030.012
nmr_identify_regions_cell0.0060.0010.006
nmr_identify_regions_urine0.0090.0000.009
nmr_integrate_regions0.0060.0010.007
nmr_interpolate_1D1.2181.0431.045
nmr_meta_add1.3971.0451.240
nmr_meta_export0.5240.5440.458
nmr_meta_get1.2260.7291.331
nmr_meta_get_column0.4940.5250.453
nmr_meta_groups0.5040.5040.438
nmr_normalize0.1760.0380.214
nmr_pca_build_model1.3091.1231.154
nmr_pca_outliers0.6310.5560.594
nmr_pca_outliers_filter0.6300.5810.617
nmr_pca_outliers_plot000
nmr_pca_outliers_robust3.7790.6233.781
nmr_pca_plots0.2510.0030.254
nmr_peak_clustering0.0460.0010.045
nmr_ppm_resolution0.0050.0000.005
nmr_read_bruker_fid000
nmr_read_samples0.9901.1190.884
nmr_zip_bruker_samples0.2050.0080.214
peaklist_accept_peaks0.0030.0000.003
permutation_test_model1.7611.1291.968
permutation_test_plot4.1342.2481.425
plot.nmr_dataset_1D0.0000.0010.001
plot_bootstrap_multimodel0.0010.0000.001
plot_interactive1.1440.9350.501
plot_plsda_multimodel0.1760.4580.336
plot_plsda_samples0.0870.1880.197
plot_vip_scores0.0000.0010.001
plot_webgl0.0010.0010.001
plsda_auroc_vip_compare0.7080.4320.921
plsda_auroc_vip_method0.0010.0000.000
ppm_resolution0.0020.0000.002
print.nmr_dataset0.5980.6120.503
print.nmr_dataset_1D1.4170.7571.474
print.nmr_dataset_peak_table0.5920.6010.565
random_subsampling0.0020.0000.001
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.5590.5650.486
sub-.nmr_dataset_1D2.1280.6051.102
sub-.nmr_dataset_peak_table0.5800.5780.579
tidy.nmr_dataset_1D0.6250.5620.585
to_ASICS0.6530.0790.734
to_ChemoSpec0.6310.6340.638
validate_nmr_dataset1.7832.2681.664
validate_nmr_dataset_family0.5350.6210.539
validate_nmr_dataset_peak_table0.0010.0000.001
zzz0.0000.0012.002