Back to Multiple platform build/check report for BioC 3.14
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-19 13:06:11 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

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 46/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.4.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_14
git_last_commit: 8ef0246
git_last_commit_date: 2021-10-26 13:05:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 3.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AlpsNMR_3.4.0.tar.gz
StartedAt: 2022-01-18 15:22:50 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 15:31:53 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 542.8 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AlpsNMR_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '3.4.0'
* 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 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          26.53   0.95   28.10
nmr_pca_plots           21.99   0.61   22.60
nmr_pca_outliers_robust  8.01   0.05    9.31
AlpsNMR-package          4.82   0.27    5.66
bp_kfold_VIP_analysis    0.62   0.05   21.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
Peak_detection          30.70   0.31   31.03
nmr_pca_plots           21.30   0.22   21.59
nmr_pca_outliers_robust  6.56   0.05    6.66
AlpsNMR-package          5.07   0.22    5.31
bp_kfold_VIP_analysis    0.65   0.10   21.27
* 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-3.14-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_3.4.0.tar.gz && rm -rf AlpsNMR.buildbin-libdir && mkdir AlpsNMR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AlpsNMR.buildbin-libdir AlpsNMR_3.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AlpsNMR_3.4.0.zip && rm AlpsNMR_3.4.0.tar.gz AlpsNMR_3.4.0.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
 10 5769k   10  585k    0     0  2466k      0  0:00:02 --:--:--  0:00:02 2469k
100 5769k  100 5769k    0     0  5748k      0  0:00:01  0:00:01 --:--:-- 5752k

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-3.14-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_3.4.0.zip
* DONE (AlpsNMR)
* installing to library 'C:/Users/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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  16.09    1.59   18.96 

AlpsNMR.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  13.89    0.85   14.73 

Example timings

AlpsNMR.Rcheck/examples_i386/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.820.275.66
MUVR_model_plot000
Peak_detection26.53 0.9528.10
Pipelines000
SummarizedExperiment_to_nmr_data_1r1.120.053.56
SummarizedExperiment_to_nmr_dataset_peak_table0.890.060.99
bp_VIP_analysis2.350.022.39
bp_kfold_VIP_analysis 0.62 0.0521.93
confusion_matrix000
file_lister0.10.00.4
files_to_rDolphin000
filter.nmr_dataset_family0.870.080.96
format.nmr_dataset0.490.030.51
format.nmr_dataset_1D0.530.010.55
format.nmr_dataset_peak_table0.800.070.91
is.nmr_dataset0.470.010.48
is.nmr_dataset_1D0.550.010.56
is.nmr_dataset_peak_table0.540.050.60
load_and_save_functions0.420.000.42
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.280.010.30
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.580.040.61
nmr_baseline_removal1.160.182.47
nmr_baseline_threshold1.570.072.97
nmr_batman0.500.030.53
nmr_batman_options000
nmr_data0.530.010.55
nmr_data_1r_to_SummarizedExperiment1.070.051.15
nmr_data_analysis0.310.000.31
nmr_data_analysis_method0.160.060.54
nmr_dataset_peak_table_to_SummarizedExperiment1.070.061.14
nmr_exclude_region000
nmr_export_data_1r0.500.040.53
nmr_identify_regions_blood0.020.000.01
nmr_identify_regions_cell0.020.000.02
nmr_identify_regions_urine0.010.000.01
nmr_integrate_regions000
nmr_interpolate_1D0.950.030.99
nmr_meta_add1.270.081.34
nmr_meta_export0.410.030.44
nmr_meta_get0.430.030.47
nmr_meta_get_column0.440.030.47
nmr_normalize0.250.010.26
nmr_pca_build_model1.080.111.21
nmr_pca_outliers1.140.071.23
nmr_pca_outliers_filter1.050.091.14
nmr_pca_outliers_plot000
nmr_pca_outliers_robust8.010.059.31
nmr_pca_plots21.99 0.6122.60
nmr_ppm_resolution0.010.000.01
nmr_read_bruker_fid000
nmr_read_samples0.860.060.94
nmr_zip_bruker_samples0.000.000.08
p_value_perm000
permutation_test_model3.670.003.67
permutation_test_plot3.250.003.25
plot.nmr_dataset_1D000
plot_bootstrap_multimodel000
plot_interactive0.580.050.69
plot_plsda_multimodel0.170.000.17
plot_plsda_samples0.110.000.11
plot_vip_scores000
plot_webgl0.020.000.02
plsda_auroc_vip_compare0.370.000.37
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.650.061.00
print.nmr_dataset_1D0.710.050.83
print.nmr_dataset_peak_table0.930.061.08
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.490.060.58
sub-.nmr_dataset_1D0.670.050.74
sub-.nmr_dataset_peak_table0.730.080.81
to_ChemoSpec0.810.100.92
validate_nmr_dataset0.940.071.00
validate_nmr_dataset_family0.520.010.53

AlpsNMR.Rcheck/examples_x64/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package5.070.225.31
MUVR_model_plot000
Peak_detection30.70 0.3131.03
Pipelines000
SummarizedExperiment_to_nmr_data_1r1.330.061.98
SummarizedExperiment_to_nmr_dataset_peak_table1.280.061.70
bp_VIP_analysis2.30.02.3
bp_kfold_VIP_analysis 0.65 0.1021.27
confusion_matrix000
file_lister0.140.010.20
files_to_rDolphin000
filter.nmr_dataset_family0.710.110.81
format.nmr_dataset0.450.030.49
format.nmr_dataset_1D0.620.070.68
format.nmr_dataset_peak_table0.910.081.13
is.nmr_dataset0.720.071.00
is.nmr_dataset_1D0.730.080.87
is.nmr_dataset_peak_table0.860.051.03
load_and_save_functions0.710.050.93
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.50.00.5
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.680.030.75
nmr_baseline_removal0.910.111.06
nmr_baseline_threshold1.330.121.45
nmr_batman0.750.050.80
nmr_batman_options000
nmr_data0.560.060.64
nmr_data_1r_to_SummarizedExperiment0.830.070.91
nmr_data_analysis0.340.000.34
nmr_data_analysis_method0.080.070.15
nmr_dataset_peak_table_to_SummarizedExperiment0.830.060.89
nmr_exclude_region000
nmr_export_data_1r0.780.090.89
nmr_identify_regions_blood0.020.000.01
nmr_identify_regions_cell0.000.020.02
nmr_identify_regions_urine0.030.000.03
nmr_integrate_regions000
nmr_interpolate_1D1.110.091.21
nmr_meta_add2.080.082.23
nmr_meta_export0.450.060.52
nmr_meta_get0.640.030.70
nmr_meta_get_column0.550.040.58
nmr_normalize0.280.000.28
nmr_pca_build_model1.670.092.11
nmr_pca_outliers0.880.030.92
nmr_pca_outliers_filter1.110.061.17
nmr_pca_outliers_plot000
nmr_pca_outliers_robust6.560.056.66
nmr_pca_plots21.30 0.2221.59
nmr_ppm_resolution0.010.000.02
nmr_read_bruker_fid000
nmr_read_samples0.880.090.97
nmr_zip_bruker_samples0.000.000.09
p_value_perm000
permutation_test_model4.260.004.27
permutation_test_plot3.610.003.61
plot.nmr_dataset_1D0.020.000.01
plot_bootstrap_multimodel000
plot_interactive0.830.031.08
plot_plsda_multimodel0.180.000.19
plot_plsda_samples0.140.000.14
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.440.000.44
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.580.070.72
print.nmr_dataset_1D0.680.060.81
print.nmr_dataset_peak_table0.920.031.09
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.450.030.54
sub-.nmr_dataset_1D0.700.050.83
sub-.nmr_dataset_peak_table0.640.010.72
to_ChemoSpec0.860.101.08
validate_nmr_dataset1.160.091.37
validate_nmr_dataset_family0.550.030.58