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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 58/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.9.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: f8b70f5
git_last_commit_date: 2024-10-29 10:53:23 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  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 kjohnson3

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: 4.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.9.0.tar.gz
StartedAt: 2024-12-23 18:07:00 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 18:08:11 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 70.9 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter.nmr_dataset_family.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.


Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
 10.246   4.278   9.508 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package0.7090.1970.680
HMDB_blood0.0020.0010.003
HMDB_cell0.0010.0000.001
HMDB_urine0.0010.0010.002
Parameters_blood0.0010.0010.001
Parameters_cell0.0000.0010.001
Parameters_urine0.0010.0000.001
Peak_detection2.7890.9502.687
Pipelines000
ROI_blood0.0010.0010.002
ROI_cell0.0000.0010.001
ROI_urine0.0010.0010.001
SummarizedExperiment_to_nmr_data_1r2.5860.2852.669
SummarizedExperiment_to_nmr_dataset_peak_table0.3320.1910.333
bp_VIP_analysis0.4270.3090.353
bp_kfold_VIP_analysis0.2770.2340.237
download_MTBLS242000
file_lister0.0210.0100.030
files_to_rDolphin000
filter.nmr_dataset_family0.3110.3190.327
format.nmr_dataset0.2850.3840.306
format.nmr_dataset_1D0.5200.2570.579
format.nmr_dataset_peak_table0.2500.1770.237
get_integration_with_metadata0.0090.0030.011
hmdb0.0160.0030.019
is.nmr_dataset0.2050.1730.179
is.nmr_dataset_1D0.2370.1570.206
is.nmr_dataset_peak_table0.2670.1910.246
load_and_save_functions0.2020.1560.175
models_stability_plot_bootstrap0.0000.0000.001
models_stability_plot_plsda0.1220.1850.146
new_nmr_dataset0.0010.0010.001
new_nmr_dataset_1D0.0000.0000.001
new_nmr_dataset_peak_table0.5440.3120.613
nmr_autophase0.0740.0420.116
nmr_baseline_estimation0.0030.0020.006
nmr_baseline_removal0.0020.0000.002
nmr_baseline_threshold0.0000.0010.000
nmr_baseline_threshold_plot0.0610.0130.076
nmr_batman0.0010.0000.002
nmr_batman_options000
nmr_build_peak_table0.0100.0020.012
nmr_data0.0140.0020.016
nmr_data_1r_to_SummarizedExperiment0.3650.2830.374
nmr_data_analysis0.1290.1600.162
nmr_dataset0.0000.0000.001
nmr_dataset_1D0.0000.0000.001
nmr_dataset_peak_table_to_SummarizedExperiment0.3650.2780.354
nmr_exclude_region0.0020.0010.002
nmr_export_data_1r0.2570.2070.240
nmr_get_peak_distances0.0020.0020.004
nmr_identify_regions_blood0.0040.0020.006
nmr_identify_regions_cell0.0030.0010.003
nmr_identify_regions_urine0.0040.0010.005
nmr_integrate_regions0.0030.0010.003
nmr_interpolate_1D0.5620.4620.525
nmr_meta_add0.5830.4820.611
nmr_meta_export0.2100.1770.189
nmr_meta_get0.2500.2560.233
nmr_meta_get_column0.2580.2750.248
nmr_meta_groups0.2240.2090.208
nmr_normalize0.0740.0320.106
nmr_pca_build_model0.6010.5260.622
nmr_pca_outliers0.3620.3030.363
nmr_pca_outliers_filter0.2960.2080.299
nmr_pca_outliers_plot0.0000.0000.001
nmr_pca_outliers_robust1.9280.3852.034
nmr_pca_plots0.1040.0030.107
nmr_peak_clustering0.0170.0000.018
nmr_ppm_resolution0.0030.0010.004
nmr_read_bruker_fid000
nmr_read_samples0.4330.4370.408
nmr_zip_bruker_samples0.1100.0140.126
peaklist_accept_peaks0.0010.0000.002
permutation_test_model0.8000.6070.633
permutation_test_plot0.9640.6600.571
plot.nmr_dataset_1D0.0000.0010.001
plot_bootstrap_multimodel0.0010.0010.001
plot_interactive0.2520.2260.249
plot_plsda_multimodel0.0910.1870.155
plot_plsda_samples0.3080.2340.123
plot_vip_scores0.0010.0010.001
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.1350.1400.278
plsda_auroc_vip_method000
ppm_resolution0.0010.0000.002
print.nmr_dataset0.2120.2130.202
print.nmr_dataset_1D0.3170.3110.335
print.nmr_dataset_peak_table0.2990.2600.290
random_subsampling0.0010.0010.002
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.2320.2510.226
sub-.nmr_dataset_1D0.2870.2890.295
sub-.nmr_dataset_peak_table0.2900.2690.292
tidy.nmr_dataset_1D0.3230.3370.347
to_ASICS0.3930.0660.461
to_ChemoSpec0.3200.3170.342
validate_nmr_dataset1.9091.3501.608
validate_nmr_dataset_family0.2840.2560.278
validate_nmr_dataset_peak_table0.0010.0000.000
zzz0.0000.0012.011