Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:57 -0400 (Fri, 15 Oct 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.
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raw results

Package 48/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.2.3  (landing page)
Luis Fernandez
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 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: 2021-10-14 19:26:51 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 19:35:52 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 541.4 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          24.34   1.21   25.71
nmr_pca_plots           22.50   0.77   23.28
nmr_pca_outliers_robust  5.97   0.08    8.11
AlpsNMR-package          4.66   0.21    5.84
bp_kfold_VIP_analysis    0.61   0.05   19.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
nmr_pca_plots           29.90   0.22   30.50
Peak_detection          23.56   0.26   23.82
nmr_pca_outliers_robust  6.25   0.01    6.29
bp_kfold_VIP_analysis    0.65   0.11   19.62
* 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  101k    0     0   384k      0  0:00:15 --:--:--  0:00:15  384k
 78 5773k   78 4541k    0     0  3597k      0  0:00:01  0:00:01 --:--:-- 3598k
100 5773k  100 5773k    0     0  3753k      0  0:00:01  0:00:01 --:--:-- 3753k

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 
  14.17    1.48   16.75 

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 
  14.25    1.00   16.56 

Example timings

AlpsNMR.Rcheck/examples_i386/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.660.215.84
MUVR_model_plot000
Peak_detection24.34 1.2125.71
Pipelines000
SummarizedExperiment_to_nmr_data_1r1.090.111.22
SummarizedExperiment_to_nmr_dataset_peak_table1.110.021.14
bp_VIP_analysis2.290.002.39
bp_kfold_VIP_analysis 0.61 0.0519.49
confusion_matrix000
file_lister0.100.013.01
files_to_rDolphin000
filter.nmr_dataset_family0.750.060.82
format.nmr_dataset0.470.020.48
format.nmr_dataset_1D0.610.050.67
format.nmr_dataset_peak_table0.650.090.75
is.nmr_dataset0.380.080.45
is.nmr_dataset_1D0.470.060.54
is.nmr_dataset_peak_table0.570.030.61
load_and_save_functions0.410.030.46
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.30.00.3
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.560.020.59
nmr_baseline_removal1.020.251.44
nmr_baseline_threshold1.450.011.47
nmr_batman0.670.071.09
nmr_batman_options000
nmr_data0.780.010.83
nmr_data_1r_to_SummarizedExperiment1.170.031.22
nmr_data_analysis0.330.000.33
nmr_data_analysis_method0.160.071.05
nmr_dataset_peak_table_to_SummarizedExperiment1.060.091.15
nmr_exclude_region000
nmr_export_data_1r0.440.110.55
nmr_identify_regions_blood0.030.000.03
nmr_identify_regions_cell000
nmr_identify_regions_urine0.010.000.02
nmr_integrate_regions000
nmr_interpolate_1D1.270.121.39
nmr_meta_add1.320.131.46
nmr_meta_export0.390.060.45
nmr_meta_get0.410.080.48
nmr_meta_get_column0.560.050.63
nmr_normalize0.330.000.33
nmr_pca_build_model1.170.121.29
nmr_pca_outliers0.640.060.71
nmr_pca_outliers_filter0.690.050.73
nmr_pca_outliers_plot000
nmr_pca_outliers_robust5.970.088.11
nmr_pca_plots22.50 0.7723.28
nmr_ppm_resolution000
nmr_read_bruker_fid000
nmr_read_samples0.830.141.11
nmr_zip_bruker_samples0.000.000.08
p_value_perm000
permutation_test_model3.80.03.8
permutation_test_plot3.460.013.48
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.660.030.72
plot_plsda_multimodel0.190.000.19
plot_plsda_samples0.120.000.12
plot_vip_scores0.020.000.02
plot_webgl000
plsda_auroc_vip_compare0.40.00.4
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.440.050.53
print.nmr_dataset_1D0.800.060.99
print.nmr_dataset_peak_table0.780.080.88
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.580.110.69
sub-.nmr_dataset_1D0.830.030.86
sub-.nmr_dataset_peak_table0.860.010.95
to_ChemoSpec0.830.100.92
validate_nmr_dataset1.170.141.34
validate_nmr_dataset_family0.600.030.63

AlpsNMR.Rcheck/examples_x64/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.490.144.63
MUVR_model_plot000
Peak_detection23.56 0.2623.82
Pipelines000
SummarizedExperiment_to_nmr_data_1r0.780.080.86
SummarizedExperiment_to_nmr_dataset_peak_table0.780.050.83
bp_VIP_analysis2.020.002.02
bp_kfold_VIP_analysis 0.65 0.1119.62
confusion_matrix000
file_lister0.080.030.11
files_to_rDolphin000
filter.nmr_dataset_family0.620.090.72
format.nmr_dataset0.750.063.12
format.nmr_dataset_1D0.880.020.95
format.nmr_dataset_peak_table0.810.091.10
is.nmr_dataset0.690.030.79
is.nmr_dataset_1D0.760.111.54
is.nmr_dataset_peak_table0.860.101.10
load_and_save_functions0.750.060.99
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.410.000.41
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.900.031.04
nmr_baseline_removal1.530.222.13
nmr_baseline_threshold2.540.002.68
nmr_batman0.430.060.50
nmr_batman_options000
nmr_data0.490.030.54
nmr_data_1r_to_SummarizedExperiment0.750.070.81
nmr_data_analysis0.30.00.3
nmr_data_analysis_method0.230.040.28
nmr_dataset_peak_table_to_SummarizedExperiment1.190.071.52
nmr_exclude_region000
nmr_export_data_1r0.850.052.49
nmr_identify_regions_blood0.010.000.01
nmr_identify_regions_cell0.000.010.02
nmr_identify_regions_urine0.030.000.03
nmr_integrate_regions000
nmr_interpolate_1D1.520.114.59
nmr_meta_add1.670.101.77
nmr_meta_export0.630.060.75
nmr_meta_get0.710.031.00
nmr_meta_get_column0.710.090.95
nmr_normalize0.330.000.33
nmr_pca_build_model1.700.081.95
nmr_pca_outliers0.650.050.70
nmr_pca_outliers_filter0.900.060.99
nmr_pca_outliers_plot000
nmr_pca_outliers_robust6.250.016.29
nmr_pca_plots29.90 0.2230.50
nmr_ppm_resolution0.000.020.02
nmr_read_bruker_fid000
nmr_read_samples1.450.091.84
nmr_zip_bruker_samples0.00.00.1
p_value_perm000
permutation_test_model3.680.023.68
permutation_test_plot3.420.003.43
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.730.040.97
plot_plsda_multimodel0.220.000.21
plot_plsda_samples0.160.000.16
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.400.000.41
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.730.000.88
print.nmr_dataset_1D0.680.080.83
print.nmr_dataset_peak_table0.780.080.89
random_subsampling0.010.000.01
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.820.082.38
sub-.nmr_dataset_1D0.780.051.78
sub-.nmr_dataset_peak_table0.900.061.03
to_ChemoSpec0.770.060.83
validate_nmr_dataset1.080.131.20
validate_nmr_dataset_family0.530.010.54