| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:54 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 44/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 3.5.0 (landing page) Sergio Oller Moreno
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: AlpsNMR |
| Version: 3.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AlpsNMR_3.5.0.tar.gz |
| StartedAt: 2022-03-17 18:25:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:30:18 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 281.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AlpsNMR_3.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/AlpsNMR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '3.5.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
nmr_pca_plots 25.25 6.53 31.82
Peak_detection 17.07 0.59 17.67
bp_kfold_VIP_analysis 0.53 0.06 17.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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-3.15-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.
AlpsNMR.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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-3.15-bioc/R/library/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
* DONE (AlpsNMR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'GCSscore' is missing or broken
done
AlpsNMR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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")
[ 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
14.79 1.43 16.31
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AUC_model | 0 | 0 | 0 | |
| AlpsNMR-package | 3.67 | 0.23 | 3.97 | |
| MUVR_model_plot | 0 | 0 | 0 | |
| Peak_detection | 17.07 | 0.59 | 17.67 | |
| Pipelines | 0 | 0 | 0 | |
| SummarizedExperiment_to_nmr_data_1r | 0.64 | 0.08 | 0.79 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 0.61 | 0.05 | 0.66 | |
| bp_VIP_analysis | 1.43 | 0.00 | 1.44 | |
| bp_kfold_VIP_analysis | 0.53 | 0.06 | 17.51 | |
| confusion_matrix | 0 | 0 | 0 | |
| file_lister | 0.07 | 0.00 | 0.05 | |
| files_to_rDolphin | 0 | 0 | 0 | |
| filter.nmr_dataset_family | 0.36 | 0.11 | 0.50 | |
| format.nmr_dataset | 0.29 | 0.03 | 0.33 | |
| format.nmr_dataset_1D | 0.38 | 0.03 | 0.44 | |
| format.nmr_dataset_peak_table | 0.42 | 0.08 | 0.51 | |
| is.nmr_dataset | 0.28 | 0.08 | 0.36 | |
| is.nmr_dataset_1D | 0.35 | 0.05 | 0.41 | |
| is.nmr_dataset_peak_table | 0.39 | 0.04 | 0.53 | |
| load_and_save_functions | 0.28 | 0.07 | 0.36 | |
| model_VIP | 0 | 0 | 0 | |
| models_stability_plot_bootstrap | 0 | 0 | 0 | |
| models_stability_plot_plsda | 0.23 | 0.00 | 0.23 | |
| new_nmr_dataset | 0 | 0 | 0 | |
| new_nmr_dataset_1D | 0 | 0 | 0 | |
| new_nmr_dataset_peak_table | 0.41 | 0.06 | 0.55 | |
| nmr_baseline_removal | 0.56 | 0.36 | 1.09 | |
| nmr_baseline_threshold | 0.98 | 0.15 | 1.14 | |
| nmr_batman | 0.35 | 0.07 | 0.41 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_data | 0.40 | 0.04 | 0.45 | |
| nmr_data_1r_to_SummarizedExperiment | 0.57 | 0.10 | 0.66 | |
| nmr_data_analysis | 0.26 | 0.00 | 0.27 | |
| nmr_data_analysis_method | 0.11 | 0.03 | 0.29 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 0.58 | 0.08 | 0.66 | |
| nmr_exclude_region | 0 | 0 | 0 | |
| nmr_export_data_1r | 0.38 | 0.06 | 0.44 | |
| nmr_identify_regions_blood | 0.01 | 0.00 | 0.01 | |
| nmr_identify_regions_cell | 0 | 0 | 0 | |
| nmr_identify_regions_urine | 0.00 | 0.02 | 0.02 | |
| nmr_integrate_regions | 0 | 0 | 0 | |
| nmr_interpolate_1D | 0.67 | 0.15 | 0.84 | |
| nmr_meta_add | 1.02 | 0.14 | 1.16 | |
| nmr_meta_export | 0.31 | 0.05 | 0.36 | |
| nmr_meta_get | 0.33 | 0.06 | 0.39 | |
| nmr_meta_get_column | 0.33 | 0.05 | 0.37 | |
| nmr_normalize | 0.18 | 0.01 | 0.21 | |
| nmr_pca_build_model | 0.77 | 0.22 | 0.98 | |
| nmr_pca_outliers | 0.48 | 0.05 | 0.57 | |
| nmr_pca_outliers_filter | 0.52 | 0.06 | 0.64 | |
| nmr_pca_outliers_plot | 0 | 0 | 0 | |
| nmr_pca_outliers_robust | 3.70 | 0.10 | 3.93 | |
| nmr_pca_plots | 25.25 | 6.53 | 31.82 | |
| nmr_ppm_resolution | 0 | 0 | 0 | |
| nmr_read_bruker_fid | 0 | 0 | 0 | |
| nmr_read_samples | 0.81 | 0.12 | 0.94 | |
| nmr_zip_bruker_samples | 0.00 | 0.00 | 0.25 | |
| p_value_perm | 0 | 0 | 0 | |
| permutation_test_model | 3.81 | 0.05 | 3.86 | |
| permutation_test_plot | 3.28 | 0.01 | 3.29 | |
| plot.nmr_dataset_1D | 0 | 0 | 0 | |
| plot_bootstrap_multimodel | 0 | 0 | 0 | |
| plot_interactive | 0.39 | 0.05 | 0.44 | |
| plot_plsda_multimodel | 0.14 | 0.00 | 0.14 | |
| plot_plsda_samples | 0.1 | 0.0 | 0.1 | |
| plot_vip_scores | 0 | 0 | 0 | |
| plot_webgl | 0 | 0 | 0 | |
| plsda_auroc_vip_compare | 0.32 | 0.00 | 0.32 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_VIP_vector | 0 | 0 | 0 | |
| ppm_resolution | 0 | 0 | 0 | |
| print.nmr_dataset | 0.30 | 0.08 | 0.38 | |
| print.nmr_dataset_1D | 0.47 | 0.08 | 0.55 | |
| print.nmr_dataset_peak_table | 0.44 | 0.11 | 0.60 | |
| random_subsampling | 0 | 0 | 0 | |
| rdCV_PLS_RF | 0 | 0 | 0 | |
| rdCV_PLS_RF_ML | 0 | 0 | 0 | |
| save_files_to_rDolphin | 0 | 0 | 0 | |
| save_profiling_output | 0 | 0 | 0 | |
| sub-.nmr_dataset | 0.34 | 0.06 | 0.43 | |
| sub-.nmr_dataset_1D | 0.39 | 0.06 | 0.45 | |
| sub-.nmr_dataset_peak_table | 0.47 | 0.11 | 0.58 | |
| to_ChemoSpec | 0.50 | 0.05 | 0.54 | |
| validate_nmr_dataset | 0.70 | 0.19 | 1.19 | |
| validate_nmr_dataset_family | 0.33 | 0.10 | 0.42 | |