Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:08 -0400 (Wed, 22 Sep 2021).

CHECK results for AlpsNMR on tokay2

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 48/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.2.3  (landing page)
Luis Fernandez
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_13
git_last_commit: 92db448
git_last_commit_date: 2021-09-16 08:28:27 -0400 (Thu, 16 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AlpsNMR
Version: 3.2.3
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AlpsNMR_3.2.3.tar.gz
StartedAt: 2021-09-21 19:04:15 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 19:13:25 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 550.1 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AlpsNMR_3.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-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 '3.2.3'
* 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                      28.20   1.59   30.03
nmr_pca_plots                       22.26   0.48   23.39
nmr_pca_outliers_robust              5.63   0.10    9.84
AlpsNMR-package                      4.82   0.37    5.81
nmr_data_1r_to_SummarizedExperiment  1.38   0.02    5.70
bp_kfold_VIP_analysis                0.58   0.04   20.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
Peak_detection          26.14   0.49   26.63
nmr_pca_plots           24.67   0.16   24.86
nmr_pca_outliers_robust  6.22   0.05    6.33
AlpsNMR-package          4.78   0.22    5.02
bp_kfold_VIP_analysis    0.66   0.07   21.67
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.



Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/AlpsNMR_3.2.3.tar.gz && rm -rf AlpsNMR.buildbin-libdir && mkdir AlpsNMR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AlpsNMR.buildbin-libdir AlpsNMR_3.2.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL AlpsNMR_3.2.3.zip && rm AlpsNMR_3.2.3.tar.gz AlpsNMR_3.2.3.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
  1 5773k    1 94525    0     0   343k      0  0:00:16 --:--:--  0:00:16  343k
 34 5773k   34 2010k    0     0  1576k      0  0:00:03  0:00:01  0:00:02 1576k
 81 5773k   81 4730k    0     0  2096k      0  0:00:02  0:00:02 --:--:-- 2096k
100 5773k  100 5773k    0     0  2240k      0  0:00:02  0:00:02 --:--:-- 2241k

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: C:/Users/biocbuild/bbs-3.13-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_3.2.3.zip
* DONE (AlpsNMR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-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 84 ]
> 
> proc.time()
   user  system elapsed 
  13.37    1.26   14.92 

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 84 ]
> 
> proc.time()
   user  system elapsed 
  14.71    0.84   15.56 

Example timings

AlpsNMR.Rcheck/examples_i386/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.820.375.81
MUVR_model_plot000
Peak_detection28.20 1.5930.03
Pipelines0.020.000.01
SummarizedExperiment_to_nmr_data_1r1.370.053.93
SummarizedExperiment_to_nmr_dataset_peak_table1.410.083.32
bp_VIP_analysis2.170.014.85
bp_kfold_VIP_analysis 0.58 0.0420.92
confusion_matrix000
file_lister0.090.000.13
files_to_rDolphin000
filter.nmr_dataset_family0.860.070.93
format.nmr_dataset0.580.020.60
format.nmr_dataset_1D0.610.030.65
format.nmr_dataset_peak_table0.580.130.71
is.nmr_dataset0.510.030.54
is.nmr_dataset_1D0.610.000.61
is.nmr_dataset_peak_table0.690.010.71
load_and_save_functions0.500.050.56
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.310.000.31
new_nmr_dataset000
new_nmr_dataset_1D0.020.000.02
new_nmr_dataset_peak_table0.720.000.71
nmr_baseline_removal1.430.231.83
nmr_baseline_threshold2.050.072.11
nmr_batman0.610.110.72
nmr_batman_options000
nmr_data1.000.091.22
nmr_data_1r_to_SummarizedExperiment1.380.025.70
nmr_data_analysis0.370.000.38
nmr_data_analysis_method0.140.060.81
nmr_dataset_peak_table_to_SummarizedExperiment1.170.041.22
nmr_exclude_region000
nmr_export_data_1r0.600.050.64
nmr_identify_regions_blood0.010.000.02
nmr_identify_regions_cell0.020.000.01
nmr_identify_regions_urine0.010.000.02
nmr_integrate_regions000
nmr_interpolate_1D1.160.101.26
nmr_meta_add1.590.071.67
nmr_meta_export0.500.070.57
nmr_meta_get0.550.060.61
nmr_meta_get_column0.550.010.56
nmr_normalize0.260.000.27
nmr_pca_build_model1.680.131.81
nmr_pca_outliers0.680.060.75
nmr_pca_outliers_filter1.050.061.11
nmr_pca_outliers_plot000
nmr_pca_outliers_robust5.630.109.84
nmr_pca_plots22.26 0.4823.39
nmr_ppm_resolution0.020.000.02
nmr_read_bruker_fid000
nmr_read_samples1.280.101.39
nmr_zip_bruker_samples0.000.000.08
p_value_perm000
permutation_test_model3.470.003.46
permutation_test_plot3.540.003.55
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.590.040.65
plot_plsda_multimodel0.220.020.24
plot_plsda_samples0.160.000.15
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.540.000.53
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution0.010.000.02
print.nmr_dataset0.610.050.65
print.nmr_dataset_1D0.660.030.69
print.nmr_dataset_peak_table0.700.060.77
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.550.050.59
sub-.nmr_dataset_1D0.570.040.62
sub-.nmr_dataset_peak_table0.720.020.74
to_ChemoSpec0.850.050.89
validate_nmr_dataset1.450.071.58
validate_nmr_dataset_family0.680.020.71

AlpsNMR.Rcheck/examples_x64/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.780.225.02
MUVR_model_plot000
Peak_detection26.14 0.4926.63
Pipelines000
SummarizedExperiment_to_nmr_data_1r1.390.031.45
SummarizedExperiment_to_nmr_dataset_peak_table1.300.031.61
bp_VIP_analysis2.310.022.33
bp_kfold_VIP_analysis 0.66 0.0721.67
confusion_matrix000
file_lister0.080.000.08
files_to_rDolphin000
filter.nmr_dataset_family0.880.030.91
format.nmr_dataset0.730.070.80
format.nmr_dataset_1D0.660.030.72
format.nmr_dataset_peak_table0.970.061.03
is.nmr_dataset0.810.131.00
is.nmr_dataset_1D0.860.040.90
is.nmr_dataset_peak_table1.000.071.07
load_and_save_functions0.710.000.74
model_VIP000
models_stability_plot_bootstrap0.010.000.01
models_stability_plot_plsda0.360.000.36
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.720.090.81
nmr_baseline_removal1.230.251.50
nmr_baseline_threshold1.720.081.80
nmr_batman0.630.030.66
nmr_batman_options000
nmr_data0.750.050.81
nmr_data_1r_to_SummarizedExperiment1.170.061.23
nmr_data_analysis0.330.000.33
nmr_data_analysis_method0.100.060.15
nmr_dataset_peak_table_to_SummarizedExperiment0.970.051.02
nmr_exclude_region0.010.000.01
nmr_export_data_1r0.580.080.66
nmr_identify_regions_blood0.020.000.02
nmr_identify_regions_cell000
nmr_identify_regions_urine000
nmr_integrate_regions0.020.000.02
nmr_interpolate_1D1.200.091.29
nmr_meta_add1.840.091.94
nmr_meta_export0.890.101.05
nmr_meta_get0.850.040.92
nmr_meta_get_column0.610.080.69
nmr_normalize0.280.020.29
nmr_pca_build_model1.530.091.63
nmr_pca_outliers1.050.081.27
nmr_pca_outliers_filter0.980.091.07
nmr_pca_outliers_plot000
nmr_pca_outliers_robust6.220.056.33
nmr_pca_plots24.67 0.1624.86
nmr_ppm_resolution000
nmr_read_bruker_fid000
nmr_read_samples2.240.092.58
nmr_zip_bruker_samples0.000.000.08
p_value_perm000
permutation_test_model3.680.023.70
permutation_test_plot3.130.003.13
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.990.011.53
plot_plsda_multimodel0.190.000.19
plot_plsda_samples0.090.020.11
plot_vip_scores000
plot_webgl0.020.000.01
plsda_auroc_vip_compare0.390.000.40
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution0.010.000.01
print.nmr_dataset0.970.031.16
print.nmr_dataset_1D1.000.041.53
print.nmr_dataset_peak_table1.060.051.40
random_subsampling0.000.020.02
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.830.031.08
sub-.nmr_dataset_1D0.650.060.72
sub-.nmr_dataset_peak_table0.720.060.78
to_ChemoSpec0.690.020.71
validate_nmr_dataset1.200.081.28
validate_nmr_dataset_family0.810.030.89