| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:04 -0400 (Wed, 15 Apr 2020).
| Package 1304/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proBatch 1.2.0 Jelena Cuklina
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: proBatch |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings proBatch_1.2.0.tar.gz |
| StartedAt: 2020-04-15 05:39:27 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:45:36 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 369.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: proBatch.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings proBatch_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/proBatch.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'proBatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proBatch' version '1.2.0'
* 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
* 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'proBatch-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dates_to_posix
> ### Title: Convert data/time to POSIXct
> ### Aliases: dates_to_posix
>
> ### ** Examples
>
> date_to_posix <- dates_to_posix(example_sample_annotation,
+ time_column = c('RunDate','RunTime'),
+ new_time_column = 'DateTime',
+ dateTimeFormat = c("%b_%d", "%H:%M:%S"))
Error: Names must be unique.
Backtrace:
x
1. +-proBatch::dates_to_posix(...)
2. | \-`%>%`(...)
3. | +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
4. | \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
5. | \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. | \-proBatch:::`_fseq`(`_lhs`)
7. | \-magrittr::freduce(value, `_function_list`)
8. | +-base::withVisible(function_list[[k]](value))
9. | \-function_list[[k]](value)
10. | +-dplyr::rename(., `:=`(!!new_time_column, dateTime))
11. | \-dplyr:::rename.data.frame(., `:=`(!!new_time_column, dateTime))
12. | \-tidyselect::vars_rename(names(.data), !!!enquos(...))
13. | \-tidyselect:::rename_impl(NULL, .vars, quo(c(...)), strict = .strict)
14. | +-tidyselect:::with_subscript_errors(...)
15. | | +-base::tryCatch(...)
16. | | | \-base:::tryCatchList(expr,
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'proBatch-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dates_to_posix
> ### Title: Convert data/time to POSIXct
> ### Aliases: dates_to_posix
>
> ### ** Examples
>
> date_to_posix <- dates_to_posix(example_sample_annotation,
+ time_column = c('RunDate','RunTime'),
+ new_time_column = 'DateTime',
+ dateTimeFormat = c("%b_%d", "%H:%M:%S"))
Error: Names must be unique.
Backtrace:
x
1. +-proBatch::dates_to_posix(...)
2. | \-`%>%`(...)
3. | +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
4. | \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
5. | \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. | \-proBatch:::`_fseq`(`_lhs`)
7. | \-magrittr::freduce(value, `_function_list`)
8. | +-base::withVisible(function_list[[k]](value))
9. | \-function_list[[k]](value)
10. | +-dplyr::rename(., `:=`(!!new_time_column, dateTime))
11. | \-dplyr:::rename.data.frame(., `:=`(!!new_time_column, dateTime))
12. | \-tidyselect::vars_rename(names(.data), !!!enquos(...))
13. | \-tidyselect:::rename_impl(NULL, .vars, quo(c(...)), strict = .strict)
14. | +-tidyselect:::with_subscript_errors(...)
15. | | +-base::tryCatch(...)
16. | | | \-base:::tryCatchList(expr,
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'spelling.R'
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 2 ERRORs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/proBatch.Rcheck/00check.log'
for details.
proBatch.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/proBatch_1.2.0.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL proBatch_1.2.0.zip && rm proBatch_1.2.0.tar.gz proBatch_1.2.0.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 834k 100 834k 0 0 4282k 0 --:--:-- --:--:-- --:--:-- 4367k
install for i386
* 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
converting help for package 'proBatch'
finding HTML links ... done
calculate_PVCA html
calculate_feature_CV html
calculate_peptide_corr_distr html
calculate_sample_corr_distr html
check_sample_consistency html
color_list_to_df html
correct_batch_effects html
create_peptide_annotation html
date_to_sample_order html
dates_to_posix html
define_sample_order html
example_peptide_annotation html
example_proteome html
example_proteome_matrix html
example_sample_annotation html
feature_level_diagnostics html
fit_nonlinear html
generate_colors_for_numeric html
long_to_matrix html
matrix_to_long html
merge_rare_levels html
normalize html
plot_CV_distr html
plot_CV_distr.df html
plot_PCA html
plot_PVCA html
plot_PVCA.df html
plot_corr_matrix html
plot_heatmap_diagnostic html
plot_heatmap_generic html
plot_hierarchical_clustering html
plot_peptide_corr_distribution html
plot_protein_corrplot html
plot_sample_corr_distribution html
plot_sample_corr_heatmap html
plot_sample_mean_or_boxplot html
plot_split_violin_with_boxplot html
prepare_PVCA_df html
proBatch html
sample_annotation_to_colors html
transform_raw_data 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 'proBatch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proBatch' as proBatch_1.2.0.zip
* DONE (proBatch)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked
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proBatch.Rcheck/tests_i386/spelling.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.26 0.01 0.25
|
proBatch.Rcheck/tests_x64/spelling.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
0.10 0.07 0.17
|
|
proBatch.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(proBatch)
>
> test_check("proBatch")
Standardizing Data across genes
== testthat results ===========================================================
[ OK: 159 | SKIPPED: 0 | WARNINGS: 31 | FAILED: 0 ]
>
> proc.time()
user system elapsed
32.89 0.70 33.57
|
proBatch.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
Standardizing Data across genes
== testthat results ===========================================================
[ OK: 159 | SKIPPED: 0 | WARNINGS: 31 | FAILED: 0 ]
>
> proc.time()
user system elapsed
32.35 0.76 33.10
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proBatch.Rcheck/examples_i386/proBatch-Ex.timings
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proBatch.Rcheck/examples_x64/proBatch-Ex.timings
|