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This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
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 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for AlpsNMR on palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz
StartedAt: 2025-03-31 22:51:32 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 23:01:28 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 596.0 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AlpsNMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlpsNMR' version '4.8.0'
* 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 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                               user system elapsed
SummarizedExperiment_to_nmr_data_1r            6.91   0.36   11.87
nmr_pca_outliers_robust                        6.06   0.31   10.86
Peak_detection                                 3.38   0.25   30.83
plsda_auroc_vip_compare                        3.24   0.08   18.75
nmr_meta_add                                   2.33   0.08   11.39
permutation_test_plot                          2.36   0.00   16.72
bp_VIP_analysis                                2.28   0.00   14.67
permutation_test_model                         2.19   0.02   15.92
validate_nmr_dataset                           2.09   0.09   10.81
nmr_pca_build_model                            2.01   0.11   10.75
nmr_interpolate_1D                             1.97   0.08   10.64
nmr_read_samples                               1.94   0.05   10.28
plot_plsda_multimodel                          1.59   0.03   10.06
plot_plsda_samples                             1.56   0.04    9.70
nmr_data_analysis                              1.57   0.02   10.35
nmr_dataset_peak_table_to_SummarizedExperiment 1.48   0.07    6.10
nmr_data_1r_to_SummarizedExperiment            1.52   0.01    6.09
AlpsNMR-package                                1.41   0.11    5.85
bp_kfold_VIP_analysis                          1.43   0.07   10.02
models_stability_plot_plsda                    1.48   0.02    9.85
SummarizedExperiment_to_nmr_dataset_peak_table 1.34   0.06    6.03
to_ChemoSpec                                   1.28   0.05    5.68
nmr_pca_outliers_filter                        1.13   0.11    5.56
tidy.nmr_dataset_1D                            1.16   0.04    5.74
is.nmr_dataset_peak_table                      1.11   0.06    5.64
new_nmr_dataset_peak_table                     1.11   0.05    6.08
nmr_pca_outliers                               1.06   0.09    5.50
validate_nmr_dataset_family                    1.10   0.03    5.37
format.nmr_dataset_peak_table                  1.05   0.06    5.62
sub-.nmr_dataset_peak_table                    1.00   0.10    5.62
nmr_export_data_1r                             1.03   0.02    5.44
filter.nmr_dataset_family                      0.99   0.03    5.63
print.nmr_dataset_peak_table                   0.97   0.04    5.04
is.nmr_dataset_1D                              0.97   0.03    5.36
plot_interactive                               0.92   0.08    5.33
nmr_autophase                                  0.95   0.04    5.43
sub-.nmr_dataset_1D                            0.94   0.04    5.41
format.nmr_dataset_1D                          0.92   0.04    5.24
print.nmr_dataset_1D                           0.94   0.02    5.30
nmr_meta_export                                0.93   0.01    5.23
nmr_meta_groups                                0.92   0.01    5.16
is.nmr_dataset                                 0.89   0.03    5.26
sub-.nmr_dataset                               0.90   0.02    5.06
format.nmr_dataset                             0.87   0.04    5.07
nmr_meta_get_column                            0.91   0.00    5.16
nmr_meta_get                                   0.86   0.02    5.25
load_and_save_functions                        0.83   0.00    5.11
* 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: OK


Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  23.35    1.32   83.23 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package1.410.115.85
HMDB_blood0.000.010.01
HMDB_cell0.010.000.01
HMDB_urine000
Parameters_blood0.000.020.02
Parameters_cell000
Parameters_urine000
Peak_detection 3.38 0.2530.83
Pipelines000
ROI_blood000
ROI_cell0.000.020.01
ROI_urine0.010.000.02
SummarizedExperiment_to_nmr_data_1r 6.91 0.3611.87
SummarizedExperiment_to_nmr_dataset_peak_table1.340.066.03
bp_VIP_analysis 2.28 0.0014.67
bp_kfold_VIP_analysis 1.43 0.0710.02
download_MTBLS242000
file_lister0.040.010.06
files_to_rDolphin000
filter.nmr_dataset_family0.990.035.63
format.nmr_dataset0.870.045.07
format.nmr_dataset_1D0.920.045.24
format.nmr_dataset_peak_table1.050.065.62
get_integration_with_metadata0.030.000.04
hmdb0.080.130.20
is.nmr_dataset0.890.035.26
is.nmr_dataset_1D0.970.035.36
is.nmr_dataset_peak_table1.110.065.64
load_and_save_functions0.830.005.11
models_stability_plot_bootstrap000
models_stability_plot_plsda1.480.029.85
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table1.110.056.08
nmr_autophase0.950.045.43
nmr_baseline_estimation0.020.000.02
nmr_baseline_removal000
nmr_baseline_threshold0.020.000.01
nmr_baseline_threshold_plot0.250.020.27
nmr_batman000
nmr_batman_options000
nmr_build_peak_table0.040.000.04
nmr_data0.080.000.08
nmr_data_1r_to_SummarizedExperiment1.520.016.09
nmr_data_analysis 1.57 0.0210.35
nmr_dataset000
nmr_dataset_1D0.020.000.01
nmr_dataset_peak_table_to_SummarizedExperiment1.480.076.10
nmr_exclude_region0.020.000.01
nmr_export_data_1r1.030.025.44
nmr_get_peak_distances000
nmr_identify_regions_blood0.020.000.02
nmr_identify_regions_cell0.010.000.01
nmr_identify_regions_urine0.010.000.01
nmr_integrate_regions0.020.000.02
nmr_interpolate_1D 1.97 0.0810.64
nmr_meta_add 2.33 0.0811.39
nmr_meta_export0.930.015.23
nmr_meta_get0.860.025.25
nmr_meta_get_column0.910.005.16
nmr_meta_groups0.920.015.16
nmr_normalize0.270.020.28
nmr_pca_build_model 2.01 0.1110.75
nmr_pca_outliers1.060.095.50
nmr_pca_outliers_filter1.130.115.56
nmr_pca_outliers_plot000
nmr_pca_outliers_robust 6.06 0.3110.86
nmr_pca_plots0.360.020.37
nmr_peak_clustering0.060.000.07
nmr_ppm_resolution0.020.000.01
nmr_read_bruker_fid000
nmr_read_samples 1.94 0.0510.28
nmr_zip_bruker_samples0.030.010.49
peaklist_accept_peaks000
permutation_test_model 2.19 0.0215.92
permutation_test_plot 2.36 0.0016.72
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.920.085.33
plot_plsda_multimodel 1.59 0.0310.06
plot_plsda_samples1.560.049.70
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare 3.24 0.0818.75
plsda_auroc_vip_method000
ppm_resolution0.010.000.02
print.nmr_dataset0.830.004.78
print.nmr_dataset_1D0.940.025.30
print.nmr_dataset_peak_table0.970.045.04
random_subsampling000
save_files_to_rDolphin0.000.000.02
save_profiling_output000
sub-.nmr_dataset0.900.025.06
sub-.nmr_dataset_1D0.940.045.41
sub-.nmr_dataset_peak_table1.000.105.62
tidy.nmr_dataset_1D1.160.045.74
to_ASICS1.000.191.18
to_ChemoSpec1.280.055.68
validate_nmr_dataset 2.09 0.0910.81
validate_nmr_dataset_family1.100.035.37
validate_nmr_dataset_peak_table000
zzz0.000.002.07