Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-19 12:04:46 -0400 (Tue, 19 Oct 2021).

CHECK results for AlpsNMR on riesling1

To the developers/maintainers of the AlpsNMR package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 46/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.3.4  (landing page)
Sergio Oller Moreno
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: master
git_last_commit: 37a58ed
git_last_commit_date: 2021-09-16 08:25:44 -0400 (Thu, 16 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AlpsNMR
Version: 3.3.4
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AlpsNMR_3.3.4.tar.gz
StartedAt: 2021-10-19 00:08:15 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 00:16:37 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 501.6 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AlpsNMR_3.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AlpsNMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlpsNMR' version '3.3.4'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
Peak_detection        17.64   0.22   17.96
nmr_pca_plots         16.64   0.25   17.00
bp_kfold_VIP_analysis  0.53   0.06   13.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
nmr_pca_plots         23.81   0.28   24.11
Peak_detection        15.65   0.22   15.87
bp_kfold_VIP_analysis  0.47   0.02   13.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'D:/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.



Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AlpsNMR_3.3.4.tar.gz && rm -rf AlpsNMR.buildbin-libdir && mkdir AlpsNMR.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AlpsNMR.buildbin-libdir AlpsNMR_3.3.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AlpsNMR_3.3.4.zip && rm AlpsNMR_3.3.4.tar.gz AlpsNMR_3.3.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 5769k    0  1135    0     0  13841      0  0:07:06 --:--:--  0:07:06 13674
 79 5769k   79 4583k    0     0  4365k      0  0:00:01  0:00:01 --:--:-- 4361k
100 5769k  100 5769k    0     0  4586k      0  0:00:01  0:00:01 --:--:-- 4586k

install for i386

* installing *source* package 'AlpsNMR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AlpsNMR'
    finding HTML links ... done
    AUC_model                               html  
    AlpsNMR-package                         html  
    HMDB_blood                              html  
    HMDB_cell                               html  
    HMDB_urine                              html  
    MUVR_model_plot                         html  
    Parameters_blood                        html  
    Parameters_cell                         html  
    Parameters_urine                        html  
    Peak_detection                          html  
    Pipelines                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.buildbin-libdir/00LOCK-AlpsNMR/00new/AlpsNMR/help/pipe_normalization.html
    ROI_blood                               html  
    ROI_cell                                html  
    ROI_urine                               html  
    SummarizedExperiment_to_nmr_data_1r     html  
    SummarizedExperiment_to_nmr_dataset_peak_table
                                            html  
    bp_VIP_analysis                         html  
    bp_kfold_VIP_analysis                   html  
    computes_peak_width_ppm                 html  
    confusion_matrix                        html  
    file_lister                             html  
    files_to_rDolphin                       html  
    filter.nmr_dataset_family               html  
    finding level-2 HTML links ... done

    format.nmr_dataset                      html  
    format.nmr_dataset_1D                   html  
    format.nmr_dataset_peak_table           html  
    hmdb                                    html  
    is.nmr_dataset                          html  
    is.nmr_dataset_1D                       html  
    is.nmr_dataset_peak_table               html  
    load_and_save_functions                 html  
    model_VIP                               html  
    models_stability_plot_bootstrap         html  
    models_stability_plot_plsda             html  
    new_nmr_dataset                         html  
    new_nmr_dataset_1D                      html  
    new_nmr_dataset_peak_table              html  
    nmr_align_find_ref                      html  
    nmr_baseline_removal                    html  
    nmr_baseline_threshold                  html  
    nmr_batman                              html  
    nmr_batman_options                      html  
    nmr_data                                html  
    nmr_data_1r_to_SummarizedExperiment     html  
    nmr_data_analysis                       html  
    nmr_data_analysis_method                html  
    nmr_dataset                             html  
    nmr_dataset_1D                          html  
    nmr_dataset_family                      html  
    nmr_dataset_peak_table                  html  
    nmr_dataset_peak_table_to_SummarizedExperiment
                                            html  
    nmr_diagnose-defunct                    html  
    nmr_exclude_region                      html  
    nmr_export_data_1r                      html  
    nmr_identify_regions_blood              html  
    nmr_identify_regions_cell               html  
    nmr_identify_regions_urine              html  
    nmr_integrate_regions                   html  
    nmr_interpolate_1D                      html  
    nmr_meta_add                            html  
    nmr_meta_export                         html  
    nmr_meta_get                            html  
    nmr_meta_get_column                     html  
    nmr_normalize                           html  
    nmr_pca_build_model                     html  
    nmr_pca_outliers                        html  
    nmr_pca_outliers_filter                 html  
    nmr_pca_outliers_plot                   html  
    nmr_pca_outliers_robust                 html  
    nmr_pca_plots                           html  
    nmr_ppm_resolution                      html  
    nmr_read_bruker_fid                     html  
    nmr_read_samples                        html  
    nmr_zip_bruker_samples                  html  
    p_value_perm                            html  
    permutation_test_model                  html  
    permutation_test_plot                   html  
    plot.nmr_dataset_1D                     html  
    plot_bootstrap_multimodel               html  
    plot_interactive                        html  
    plot_plsda_multimodel                   html  
    plot_plsda_samples                      html  
    plot_vip_scores                         html  
    plot_webgl                              html  
    plsda_auroc_vip_compare                 html  
    plsda_auroc_vip_method                  html  
    ppm_VIP_vector                          html  
    ppm_resolution                          html  
    print.nmr_dataset                       html  
    print.nmr_dataset_1D                    html  
    print.nmr_dataset_peak_table            html  
    random_subsampling                      html  
    rdCV_PLS_RF                             html  
    rdCV_PLS_RF_ML                          html  
    read_bruker_sample                      html  
    regions_from_peak_table                 html  
    save_files_to_rDolphin                  html  
    save_profiling_output                   html  
    sub-.nmr_dataset                        html  
    sub-.nmr_dataset_1D                     html  
    sub-.nmr_dataset_peak_table             html  
    to_ChemoSpec                            html  
    validate_nmr_dataset                    html  
    validate_nmr_dataset_family             html  
*** 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

install for x64

* installing *source* package 'AlpsNMR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AlpsNMR' as AlpsNMR_3.3.4.zip
* DONE (AlpsNMR)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'AlpsNMR' successfully unpacked and MD5 sums checked

Tests output

AlpsNMR.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: future
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> 
> test_check("AlpsNMR")
== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
   8.35    0.92    9.29 

AlpsNMR.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: future
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> 
> test_check("AlpsNMR")
== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
   9.34    0.75   10.14 

Example timings

AlpsNMR.Rcheck/examples_i386/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package3.110.093.21
MUVR_model_plot000
Peak_detection17.64 0.2217.96
Pipelines000
SummarizedExperiment_to_nmr_data_1r0.830.050.89
SummarizedExperiment_to_nmr_dataset_peak_table0.920.060.99
bp_VIP_analysis1.390.001.39
bp_kfold_VIP_analysis 0.53 0.0613.58
confusion_matrix000
file_lister0.060.020.08
files_to_rDolphin000
filter.nmr_dataset_family0.410.040.45
format.nmr_dataset0.300.070.39
format.nmr_dataset_1D0.420.060.48
format.nmr_dataset_peak_table0.510.060.58
is.nmr_dataset0.430.060.49
is.nmr_dataset_1D0.540.020.56
is.nmr_dataset_peak_table0.530.030.56
load_and_save_functions0.290.050.33
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.180.000.19
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.330.080.41
nmr_baseline_removal0.680.110.80
nmr_baseline_threshold1.220.041.26
nmr_batman0.410.030.44
nmr_batman_options000
nmr_data0.440.040.47
nmr_data_1r_to_SummarizedExperiment0.720.070.79
nmr_data_analysis0.310.000.32
nmr_data_analysis_method0.100.080.41
nmr_dataset_peak_table_to_SummarizedExperiment0.610.100.70
nmr_exclude_region0.010.000.02
nmr_export_data_1r0.360.010.37
nmr_identify_regions_blood0.020.000.02
nmr_identify_regions_cell000
nmr_identify_regions_urine0.010.000.01
nmr_integrate_regions000
nmr_interpolate_1D0.690.080.85
nmr_meta_add0.840.120.97
nmr_meta_export0.250.070.31
nmr_meta_get0.290.030.31
nmr_meta_get_column0.280.040.33
nmr_normalize0.170.000.17
nmr_pca_build_model0.770.100.86
nmr_pca_outliers0.360.060.42
nmr_pca_outliers_filter0.450.080.57
nmr_pca_outliers_plot000
nmr_pca_outliers_robust3.640.053.68
nmr_pca_plots16.64 0.2517.00
nmr_ppm_resolution0.000.010.02
nmr_read_bruker_fid000
nmr_read_samples0.550.050.59
nmr_zip_bruker_samples0.000.000.02
p_value_perm000
permutation_test_model2.000.012.01
permutation_test_plot2.060.002.07
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.280.080.36
plot_plsda_multimodel0.110.000.11
plot_plsda_samples0.080.000.07
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.260.000.27
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.240.080.31
print.nmr_dataset_1D0.340.020.36
print.nmr_dataset_peak_table0.380.040.42
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.260.030.30
sub-.nmr_dataset_1D0.350.040.39
sub-.nmr_dataset_peak_table0.360.040.41
to_ChemoSpec0.400.060.47
validate_nmr_dataset0.550.100.73
validate_nmr_dataset_family0.340.010.36

AlpsNMR.Rcheck/examples_x64/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package3.470.053.51
MUVR_model_plot000
Peak_detection15.65 0.2215.87
Pipelines000
SummarizedExperiment_to_nmr_data_1r0.580.030.61
SummarizedExperiment_to_nmr_dataset_peak_table0.530.080.61
bp_VIP_analysis1.310.001.32
bp_kfold_VIP_analysis 0.47 0.0213.67
confusion_matrix000
file_lister0.030.000.03
files_to_rDolphin000
filter.nmr_dataset_family0.300.080.37
format.nmr_dataset0.280.010.30
format.nmr_dataset_1D0.330.000.33
format.nmr_dataset_peak_table0.300.110.40
is.nmr_dataset0.190.090.28
is.nmr_dataset_1D0.300.040.33
is.nmr_dataset_peak_table0.390.010.41
load_and_save_functions0.280.000.28
model_VIP0.020.000.01
models_stability_plot_bootstrap000
models_stability_plot_plsda0.200.000.21
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.360.030.39
nmr_baseline_removal0.610.100.70
nmr_baseline_threshold0.900.040.98
nmr_batman0.320.030.63
nmr_batman_options000
nmr_data0.320.050.45
nmr_data_1r_to_SummarizedExperiment0.520.050.56
nmr_data_analysis0.220.010.24
nmr_data_analysis_method0.090.020.11
nmr_dataset_peak_table_to_SummarizedExperiment0.560.010.58
nmr_exclude_region000
nmr_export_data_1r0.390.020.41
nmr_identify_regions_blood0.020.000.01
nmr_identify_regions_cell0.010.000.02
nmr_identify_regions_urine000
nmr_integrate_regions0.020.000.02
nmr_interpolate_1D0.640.050.68
nmr_meta_add0.900.091.00
nmr_meta_export0.320.000.32
nmr_meta_get0.290.030.32
nmr_meta_get_column0.300.050.35
nmr_normalize0.170.000.17
nmr_pca_build_model0.750.090.87
nmr_pca_outliers0.410.070.72
nmr_pca_outliers_filter0.420.040.47
nmr_pca_outliers_plot000
nmr_pca_outliers_robust3.360.083.43
nmr_pca_plots23.81 0.2824.11
nmr_ppm_resolution0.020.000.02
nmr_read_bruker_fid000
nmr_read_samples0.550.080.62
nmr_zip_bruker_samples0.000.000.04
p_value_perm000
permutation_test_model2.210.002.21
permutation_test_plot2.210.002.21
plot.nmr_dataset_1D0.010.000.01
plot_bootstrap_multimodel000
plot_interactive0.320.030.35
plot_plsda_multimodel0.100.010.12
plot_plsda_samples0.070.020.08
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.250.000.25
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution0.010.000.02
print.nmr_dataset0.300.010.31
print.nmr_dataset_1D0.280.050.34
print.nmr_dataset_peak_table0.380.030.41
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.270.030.36
sub-.nmr_dataset_1D0.290.070.36
sub-.nmr_dataset_peak_table0.390.030.42
to_ChemoSpec0.410.040.53
validate_nmr_dataset0.590.100.70
validate_nmr_dataset_family0.310.040.36