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This page was generated on 2024-06-20 12:14 -0400 (Thu, 20 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
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 57/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.7.1  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: ac7cb18
git_last_commit_date: 2024-06-09 06:57:22 -0400 (Sun, 09 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped


CHECK results for AlpsNMR on nebbiolo2

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: 4.7.1
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_4.7.1.tar.gz
StartedAt: 2024-06-19 20:30:16 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 20:34:34 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 258.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

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### 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_4.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.7.1’
* 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                      7.810  1.627   4.539
SummarizedExperiment_to_nmr_data_1r 6.575  0.657   6.703
is.nmr_dataset_peak_table           3.397  2.538   2.952
nmr_pca_outliers_robust             4.822  0.857   4.867
* 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

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


* installing to library ‘/home/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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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 
 25.813  10.978  23.811 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package1.6510.3391.483
HMDB_blood0.0030.0040.006
HMDB_cell0.0020.0000.002
HMDB_urine0.0040.0000.004
Parameters_blood0.0010.0000.001
Parameters_cell0.0020.0000.002
Parameters_urine0.0010.0000.002
Peak_detection7.8101.6274.539
Pipelines0.0010.0000.002
ROI_blood0.0030.0000.003
ROI_cell0.0030.0000.003
ROI_urine0.0030.0000.003
SummarizedExperiment_to_nmr_data_1r6.5750.6576.703
SummarizedExperiment_to_nmr_dataset_peak_table0.9520.3880.789
bp_VIP_analysis1.2260.7270.727
bp_kfold_VIP_analysis0.7180.4050.436
download_MTBLS242000
file_lister0.0530.0160.068
files_to_rDolphin000
filter.nmr_dataset_family3.0401.6752.216
format.nmr_dataset0.6900.3710.463
format.nmr_dataset_1D0.6900.3900.523
format.nmr_dataset_peak_table0.7490.4800.577
get_integration_with_metadata0.0240.0040.028
hmdb0.0490.0080.057
is.nmr_dataset0.5880.4350.435
is.nmr_dataset_1D0.7210.4870.580
is.nmr_dataset_peak_table3.3972.5382.952
load_and_save_functions0.6250.4080.454
models_stability_plot_bootstrap0.0020.0000.002
models_stability_plot_plsda0.2870.3720.311
new_nmr_dataset0.0010.0000.001
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.7950.5050.609
nmr_autophase0.1710.0950.297
nmr_baseline_estimation0.0280.0370.010
nmr_baseline_removal0.0050.0000.005
nmr_baseline_threshold0.0010.0000.001
nmr_baseline_threshold_plot0.2120.0190.232
nmr_batman0.0030.0000.003
nmr_batman_options000
nmr_build_peak_table0.0240.0120.036
nmr_data0.0440.0040.047
nmr_data_1r_to_SummarizedExperiment0.9440.5060.859
nmr_data_analysis0.3370.3810.319
nmr_dataset000
nmr_dataset_1D0.0010.0000.001
nmr_dataset_peak_table_to_SummarizedExperiment0.9610.4080.798
nmr_exclude_region0.0050.0000.005
nmr_export_data_1r0.6080.4200.480
nmr_get_peak_distances0.0030.0040.007
nmr_identify_regions_blood0.0260.0000.026
nmr_identify_regions_cell0.0090.0000.008
nmr_identify_regions_urine0.0120.0000.012
nmr_integrate_regions0.0090.0000.010
nmr_interpolate_1D1.4370.7801.013
nmr_meta_add1.7240.9581.407
nmr_meta_export0.6800.4630.474
nmr_meta_get0.6150.4470.468
nmr_meta_get_column0.7410.4450.516
nmr_meta_groups0.6320.4560.484
nmr_normalize0.2290.0440.272
nmr_pca_build_model1.5361.0521.327
nmr_pca_outliers0.9420.4390.699
nmr_pca_outliers_filter0.9310.5160.737
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.8220.8574.867
nmr_pca_plots0.3210.0160.337
nmr_peak_clustering0.0570.0040.062
nmr_ppm_resolution0.0070.0000.007
nmr_read_bruker_fid000
nmr_read_samples1.2950.9040.931
nmr_zip_bruker_samples0.2460.0170.265
peaklist_accept_peaks0.0020.0010.004
permutation_test_model2.4981.3961.698
permutation_test_plot3.3251.6211.498
plot.nmr_dataset_1D0.0020.0000.001
plot_bootstrap_multimodel0.0020.0000.001
plot_interactive1.7420.8930.637
plot_plsda_multimodel0.2330.4660.341
plot_plsda_samples0.1510.1700.267
plot_vip_scores0.0010.0000.001
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.5370.4610.777
plsda_auroc_vip_method0.0010.0000.000
ppm_resolution0.0030.0000.003
print.nmr_dataset0.6570.5590.563
print.nmr_dataset_1D0.6910.6150.639
print.nmr_dataset_peak_table1.6070.9551.813
random_subsampling0.0000.0010.001
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.5280.4890.438
sub-.nmr_dataset_1D0.6840.3940.516
sub-.nmr_dataset_peak_table0.7760.4650.593
tidy.nmr_dataset_1D0.7600.4390.602
to_ASICS0.8600.0800.939
to_ChemoSpec0.7280.4470.630
validate_nmr_dataset1.5150.9131.130
validate_nmr_dataset_family0.6540.5560.570
validate_nmr_dataset_peak_table0.0010.0000.001
zzz0.0010.0002.001