Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:09 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (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: 2022-04-12 15:30:07 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:39:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 564.7 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 4.1.3 (2022-03-10)
* 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 '3.4.0'
* 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
nmr_pca_plots           30.52   1.24   31.81
Peak_detection          27.28   1.14   31.83
nmr_pca_outliers_robust  5.78   0.03   10.08
AlpsNMR-package          4.21   0.36    5.12
bp_kfold_VIP_analysis    0.58   0.06   20.66
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
Peak_detection          24.88   0.25   26.12
nmr_pca_plots           21.06   0.30   21.36
nmr_pca_outliers_robust  6.33   0.05    6.42
bp_kfold_VIP_analysis    0.62   0.07   23.50
* 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
  0 5769k    0 14659    0     0   122k      0  0:00:47 --:--:--  0:00:47  122k
 23 5769k   23 1381k    0     0  1235k      0  0:00:04  0:00:01  0:00:03 1235k
 62 5769k   62 3620k    0     0  1723k      0  0:00:03  0:00:02  0:00:01 1723k
100 5769k  100 5769k    0     0  2056k      0  0:00:02  0:00:02 --:--:-- 2056k

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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]

== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
  12.23    1.39   13.82 

AlpsNMR.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]

== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
  16.32    0.89   17.98 

Example timings

AlpsNMR.Rcheck/examples_i386/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.210.365.12
MUVR_model_plot000
Peak_detection27.28 1.1431.83
Pipelines000
SummarizedExperiment_to_nmr_data_1r0.940.050.99
SummarizedExperiment_to_nmr_dataset_peak_table1.010.081.51
bp_VIP_analysis2.270.022.33
bp_kfold_VIP_analysis 0.58 0.0620.66
confusion_matrix000
file_lister0.070.010.14
files_to_rDolphin000
filter.nmr_dataset_family0.720.130.86
format.nmr_dataset0.470.030.50
format.nmr_dataset_1D0.520.080.62
format.nmr_dataset_peak_table0.650.120.83
is.nmr_dataset0.440.070.52
is.nmr_dataset_1D0.550.060.60
is.nmr_dataset_peak_table0.540.060.61
load_and_save_functions0.440.080.52
model_VIP000
models_stability_plot_bootstrap0.020.000.02
models_stability_plot_plsda0.470.000.46
new_nmr_dataset000
new_nmr_dataset_1D0.010.000.02
new_nmr_dataset_peak_table0.800.110.91
nmr_baseline_removal1.120.311.82
nmr_baseline_threshold1.990.092.08
nmr_batman0.590.054.66
nmr_batman_options000
nmr_data0.470.090.56
nmr_data_1r_to_SummarizedExperiment0.890.080.97
nmr_data_analysis0.410.020.42
nmr_data_analysis_method0.120.060.47
nmr_dataset_peak_table_to_SummarizedExperiment1.270.051.39
nmr_exclude_region0.010.000.02
nmr_export_data_1r0.660.030.70
nmr_identify_regions_blood0.020.000.02
nmr_identify_regions_cell0.010.000.01
nmr_identify_regions_urine0.020.000.02
nmr_integrate_regions0.010.000.01
nmr_interpolate_1D1.240.111.35
nmr_meta_add1.870.111.98
nmr_meta_export0.440.040.48
nmr_meta_get0.530.050.58
nmr_meta_get_column0.480.050.53
nmr_normalize0.30.00.3
nmr_pca_build_model1.530.111.64
nmr_pca_outliers0.860.080.93
nmr_pca_outliers_filter1.030.041.11
nmr_pca_outliers_plot000
nmr_pca_outliers_robust 5.78 0.0310.08
nmr_pca_plots30.52 1.2431.81
nmr_ppm_resolution0.010.000.02
nmr_read_bruker_fid000
nmr_read_samples1.050.081.14
nmr_zip_bruker_samples0.000.000.08
p_value_perm000
permutation_test_model3.780.003.78
permutation_test_plot4.000.014.02
plot.nmr_dataset_1D000
plot_bootstrap_multimodel0.020.000.01
plot_interactive0.810.131.11
plot_plsda_multimodel0.20.00.2
plot_plsda_samples0.160.000.16
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.470.000.47
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.590.040.80
print.nmr_dataset_1D0.810.041.03
print.nmr_dataset_peak_table1.000.061.48
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.660.060.78
sub-.nmr_dataset_1D0.870.061.16
sub-.nmr_dataset_peak_table0.940.081.16
to_ChemoSpec1.020.111.25
validate_nmr_dataset1.610.163.20
validate_nmr_dataset_family0.840.071.23

AlpsNMR.Rcheck/examples_x64/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model000
AlpsNMR-package4.790.215.00
MUVR_model_plot000
Peak_detection24.88 0.2526.12
Pipelines000
SummarizedExperiment_to_nmr_data_1r1.320.031.83
SummarizedExperiment_to_nmr_dataset_peak_table1.270.071.80
bp_VIP_analysis202
bp_kfold_VIP_analysis 0.62 0.0723.50
confusion_matrix000
file_lister0.110.000.11
files_to_rDolphin000
filter.nmr_dataset_family0.710.090.79
format.nmr_dataset0.450.050.52
format.nmr_dataset_1D0.640.090.76
format.nmr_dataset_peak_table0.550.100.69
is.nmr_dataset0.720.101.11
is.nmr_dataset_1D0.840.071.16
is.nmr_dataset_peak_table0.660.040.70
load_and_save_functions0.780.050.98
model_VIP000
models_stability_plot_bootstrap000
models_stability_plot_plsda0.450.020.47
new_nmr_dataset000
new_nmr_dataset_1D000
new_nmr_dataset_peak_table0.610.060.77
nmr_baseline_removal1.420.111.73
nmr_baseline_threshold1.780.112.06
nmr_batman0.500.040.55
nmr_batman_options000
nmr_data0.530.070.59
nmr_data_1r_to_SummarizedExperiment0.800.060.86
nmr_data_analysis0.370.000.38
nmr_data_analysis_method0.100.060.15
nmr_dataset_peak_table_to_SummarizedExperiment0.860.030.89
nmr_exclude_region000
nmr_export_data_1r0.460.030.50
nmr_identify_regions_blood0.040.000.03
nmr_identify_regions_cell000
nmr_identify_regions_urine0.010.000.02
nmr_integrate_regions000
nmr_interpolate_1D1.000.051.06
nmr_meta_add1.470.061.55
nmr_meta_export0.480.000.48
nmr_meta_get0.640.030.72
nmr_meta_get_column0.710.080.78
nmr_normalize0.400.000.41
nmr_pca_build_model1.440.161.61
nmr_pca_outliers0.640.060.70
nmr_pca_outliers_filter0.950.010.97
nmr_pca_outliers_plot000
nmr_pca_outliers_robust6.330.056.42
nmr_pca_plots21.06 0.3021.36
nmr_ppm_resolution0.020.000.02
nmr_read_bruker_fid000
nmr_read_samples0.730.080.81
nmr_zip_bruker_samples0.000.000.08
p_value_perm000
permutation_test_model4.050.014.06
permutation_test_plot3.670.003.67
plot.nmr_dataset_1D000
plot_bootstrap_multimodel0.020.000.02
plot_interactive0.700.081.02
plot_plsda_multimodel0.230.000.23
plot_plsda_samples0.160.000.16
plot_vip_scores000
plot_webgl000
plsda_auroc_vip_compare0.450.010.50
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution000
print.nmr_dataset0.640.070.70
print.nmr_dataset_1D0.770.031.02
print.nmr_dataset_peak_table1.010.051.64
random_subsampling000
rdCV_PLS_RF000
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset1.580.003.62
sub-.nmr_dataset_1D0.750.090.88
sub-.nmr_dataset_peak_table0.610.050.65
to_ChemoSpec0.720.000.72
validate_nmr_dataset1.170.042.78
validate_nmr_dataset_family0.580.050.63