| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:29:52 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the AlpsNMR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 48/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 3.0.6 (landing page) Luis Fernandez
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: AlpsNMR |
| Version: 3.0.6 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AlpsNMR_3.0.6.tar.gz |
| StartedAt: 2021-05-06 00:23:34 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:32:40 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 546.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AlpsNMR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AlpsNMR_3.0.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '3.0.6'
* 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 ... WARNING
Undocumented arguments in documentation object 'MUVR_model_plot'
'MVObj' 'model' 'factCols' 'sampLabels' 'ylim'
Undocumented arguments in documentation object 'confusion_matrix'
'MVObj' 'model'
Undocumented arguments in documentation object 'model_VIP'
'model'
Undocumented arguments in documentation object 'rdCV_PLS_RF'
'X' 'Y' 'ID' 'scale' 'nRep' 'nOuter' 'nInner' 'varRatio' 'DA'
'fitness' 'method' 'nCompMax' 'methParam' 'ML' 'modReturn' 'logg'
'parallel'
Undocumented arguments in documentation object 'rdCV_PLS_RF_ML'
'scale' 'nRep' 'nOuter' 'nInner' 'varRatio' 'DA' 'fitness' 'method'
'ML' 'modReturn' 'logg' 'parallel'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... ERROR
Running examples in 'AlpsNMR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nmr_pca_plots
> ### Title: Plotting functions for PCA
> ### Aliases: nmr_pca_plots nmr_pca_plot_variance nmr_pca_scoreplot
> ### nmr_pca_loadingplot
>
> ### ** Examples
>
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
> dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
> model <- nmr_pca_build_model(dataset_1D)
> nmr_pca_plot_variance(model)
>
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
> dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
> model <- nmr_pca_build_model(dataset_1D)
> nmr_pca_scoreplot(dataset_1D, model)
Error: Join columns must be present in data.
x Problem with `NMRExperiment`.
Backtrace:
x
1. +-AlpsNMR::nmr_pca_scoreplot(dataset_1D, model)
2. | \-`%>%`(...)
3. +-dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
4. \-dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
5. \-dplyr:::join_mutate(...)
6. \-dplyr:::join_cols(...)
7. \-dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
8. \-dplyr:::check_join_vars(by$x, x_names)
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'AlpsNMR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nmr_pca_plots
> ### Title: Plotting functions for PCA
> ### Aliases: nmr_pca_plots nmr_pca_plot_variance nmr_pca_scoreplot
> ### nmr_pca_loadingplot
>
> ### ** Examples
>
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
> dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
> model <- nmr_pca_build_model(dataset_1D)
> nmr_pca_plot_variance(model)
>
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
> dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
> model <- nmr_pca_build_model(dataset_1D)
> nmr_pca_scoreplot(dataset_1D, model)
Error: Join columns must be present in data.
x Problem with `NMRExperiment`.
Backtrace:
x
1. +-AlpsNMR::nmr_pca_scoreplot(dataset_1D, model)
2. | \-`%>%`(...)
3. +-dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
4. \-dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
5. \-dplyr:::join_mutate(...)
6. \-dplyr:::join_cols(...)
7. \-dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
8. \-dplyr:::check_join_vars(by$x, x_names)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
x Problem with `NMRExperiment`.
Backtrace:
x
1. +-AlpsNMR::nmr_pca_scoreplot(dataset, pca_built) test-outliers.R:12:2
2. | \-`%>%`(...)
3. +-dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
4. \-dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
5. \-dplyr:::join_mutate(...)
6. \-dplyr:::join_cols(...)
7. \-dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
8. \-dplyr:::check_join_vars(by$x, x_names)
[ FAIL 1 | WARN 2 | SKIP 1 | PASS 73 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
x Problem with `NMRExperiment`.
Backtrace:
x
1. +-AlpsNMR::nmr_pca_scoreplot(dataset, pca_built) test-outliers.R:12:2
2. | \-`%>%`(...)
3. +-dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
4. \-dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
5. \-dplyr:::join_mutate(...)
6. \-dplyr:::join_cols(...)
7. \-dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
8. \-dplyr:::check_join_vars(by$x, x_names)
[ FAIL 1 | WARN 2 | SKIP 1 | PASS 73 ]
Error: Test failures
Execution halted
* 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: 4 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.
AlpsNMR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/AlpsNMR_3.0.6.tar.gz && rm -rf AlpsNMR.buildbin-libdir && mkdir AlpsNMR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AlpsNMR.buildbin-libdir AlpsNMR_3.0.6.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AlpsNMR_3.0.6.zip && rm AlpsNMR_3.0.6.tar.gz AlpsNMR_3.0.6.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3254k 100 3254k 0 0 31.8M 0 --:--:-- --:--:-- --:--:-- 32.1M
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
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
** 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_3.0.6.zip
* DONE (AlpsNMR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AlpsNMR' successfully unpacked and MD5 sums checked
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AlpsNMR.Rcheck/tests_i386/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
== Failed tests ================================================================
-- Error (test-outliers.R:12:3): nmr_pca_outliers_robust works -----------------
Error: Join columns must be present in data.
x Problem with `NMRExperiment`.
Backtrace:
x
1. +-AlpsNMR::nmr_pca_scoreplot(dataset, pca_built) test-outliers.R:12:2
2. | \-`%>%`(...)
3. +-dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
4. \-dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
5. \-dplyr:::join_mutate(...)
6. \-dplyr:::join_cols(...)
7. \-dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
8. \-dplyr:::check_join_vars(by$x, x_names)
[ FAIL 1 | WARN 2 | SKIP 1 | PASS 73 ]
Error: Test failures
Execution halted
|
AlpsNMR.Rcheck/tests_x64/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
== Failed tests ================================================================
-- Error (test-outliers.R:12:3): nmr_pca_outliers_robust works -----------------
Error: Join columns must be present in data.
x Problem with `NMRExperiment`.
Backtrace:
x
1. +-AlpsNMR::nmr_pca_scoreplot(dataset, pca_built) test-outliers.R:12:2
2. | \-`%>%`(...)
3. +-dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
4. \-dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
5. \-dplyr:::join_mutate(...)
6. \-dplyr:::join_cols(...)
7. \-dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
8. \-dplyr:::check_join_vars(by$x, x_names)
[ FAIL 1 | WARN 2 | SKIP 1 | PASS 73 ]
Error: Test failures
Execution halted
|
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AlpsNMR.Rcheck/examples_i386/AlpsNMR-Ex.timings
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AlpsNMR.Rcheck/examples_x64/AlpsNMR-Ex.timings
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