| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:44 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 proBatch package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1508/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| proBatch 1.15.0 (landing page) Chloe H. Lee
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
| Package: proBatch |
| Version: 1.15.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:proBatch.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings proBatch_1.15.0.tar.gz |
| StartedAt: 2022-12-29 02:25:57 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 02:29:58 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 241.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: proBatch.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:proBatch.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings proBatch_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/proBatch.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'proBatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proBatch' version '1.15.0'
* 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 'proBatch' 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'proBatch-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_protein_corrplot
> ### Title: Peptide correlation matrix (heatmap)
> ### Aliases: plot_protein_corrplot
>
> ### ** Examples
>
> protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix,
+ protein_name = 'Haao', peptide_annotation = example_peptide_annotation,
+ protein_col = 'Gene')
Warning in plot_corr_matrix(corr_matrix, annotation = peptide_annotation, :
color_list for annotation (cols & rows) not defined, inferring automatically.
Numeric/factor columns are guessed, for more controlled color mapping use
sample_annotation_to_colors()
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col, :
The following columns will not be mapped to colors: Gene if these have to be mapped, please assign
them to factor, date or numeric
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col, :
numeric columns not specified,
extracting numeric columns from factors
converting columns to corresponding classes
(factor, numeric)
>
> protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix,
+ protein_name = c('Haao', 'Dhtkd1'),
+ peptide_annotation = example_peptide_annotation,
+ protein_col = 'Gene', factors_to_plot = 'Gene')
Warning in plot_corr_matrix(corr_matrix, annotation = peptide_annotation, :
color_list for annotation (cols & rows) not defined, inferring automatically.
Numeric/factor columns are guessed, for more controlled color mapping use
sample_annotation_to_colors()
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col, :
The following columns will not be mapped to colors: ProteinName if these have to be mapped, please assign
them to factor, date or numeric
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col, :
numeric columns not specified,
extracting numeric columns from factors
converting columns to corresponding classes
(factor, numeric)
Error in if (is.na(main)) { : the condition has length > 1
Calls: plot_protein_corrplot ... plot_heatmap_generic -> pheatmap -> heatmap_motor -> lo
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'spelling.R'
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 ERROR
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/proBatch.Rcheck/00check.log'
for details.
proBatch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL proBatch ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'proBatch' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (proBatch)
proBatch.Rcheck/tests/spelling.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.14 0.10 0.18
proBatch.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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(proBatch)
>
> test_check("proBatch")
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 159 ]
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 159 ]
>
> proc.time()
user system elapsed
30.01 0.92 30.93
proBatch.Rcheck/proBatch-Ex.timings
| name | user | system | elapsed | |
| calculate_PVCA | 16.08 | 0.05 | 16.13 | |
| calculate_feature_CV | 0.39 | 0.03 | 0.42 | |
| calculate_peptide_corr_distr | 0.03 | 0.00 | 0.03 | |
| calculate_sample_corr_distr | 0.48 | 0.03 | 0.52 | |
| check_sample_consistency | 0.02 | 0.00 | 0.01 | |
| correct_batch_effects | 5.03 | 0.03 | 5.07 | |
| create_peptide_annotation | 0 | 0 | 0 | |
| date_to_sample_order | 0.12 | 0.00 | 0.12 | |
| dates_to_posix | 0.02 | 0.00 | 0.02 | |
| define_sample_order | 0.02 | 0.00 | 0.01 | |
| feature_level_diagnostics | 4.13 | 0.06 | 4.19 | |
| fit_nonlinear | 0 | 0 | 0 | |
| long_to_matrix | 0.03 | 0.00 | 0.03 | |
| matrix_to_long | 0.01 | 0.00 | 0.01 | |
| normalize | 0.08 | 0.00 | 0.08 | |
| plot_CV_distr | 0.67 | 0.02 | 0.69 | |
| plot_PCA | 0.64 | 0.01 | 0.65 | |
| plot_PVCA | 15.30 | 0.08 | 15.38 | |
| plot_PVCA.df | 16.38 | 0.02 | 16.41 | |
| plot_corr_matrix | 0.07 | 0.00 | 0.07 | |
| plot_heatmap_diagnostic | 1.36 | 0.03 | 1.39 | |
| plot_heatmap_generic | 0.55 | 0.00 | 0.55 | |
| plot_hierarchical_clustering | 0.40 | 0.02 | 0.42 | |
| plot_peptide_corr_distribution | 1.00 | 0.03 | 1.03 | |