Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-27 11:06:15 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 proBatch on nebbiolo1


To the developers/maintainers of the proBatch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proBatch.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.

raw results

Package 1455/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proBatch 1.11.0  (landing page)
Chloe H. Lee
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/proBatch
git_branch: master
git_last_commit: f9dca1a
git_last_commit_date: 2021-10-26 12:50:21 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: proBatch
Version: 1.11.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings proBatch_1.11.0.tar.gz
StartedAt: 2022-01-26 20:36:44 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 20:41:37 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 293.8 seconds
RetCode: 0
Status:   OK  
CheckDir: proBatch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings proBatch_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/proBatch.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
calculate_PVCA            15.791  0.352  16.146
plot_PVCA                 15.288  0.096  15.385
plot_PVCA.df              15.220  0.064  15.284
prepare_PVCA_df           15.168  0.096  15.263
feature_level_diagnostics  6.000  0.156   6.155
correct_batch_effects      5.425  0.160   5.599
* 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: OK


Installation output

proBatch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL proBatch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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)

Tests output

proBatch.Rcheck/tests/spelling.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.152   0.037   0.176 

proBatch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 30 | SKIP 0 | PASS 159 ]

[ FAIL 0 | WARN 30 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
 33.905   1.253  35.165 

Example timings

proBatch.Rcheck/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA15.791 0.35216.146
calculate_feature_CV0.9520.0881.040
calculate_peptide_corr_distr0.0250.0030.028
calculate_sample_corr_distr0.5360.0080.544
check_sample_consistency0.5720.0400.611
correct_batch_effects5.4250.1605.599
create_peptide_annotation0.0080.0000.009
date_to_sample_order0.1150.0000.115
dates_to_posix0.0100.0000.009
define_sample_order0.0120.0000.012
feature_level_diagnostics6.0000.1566.155
fit_nonlinear0.0090.0000.008
long_to_matrix0.0410.0000.041
matrix_to_long0.0110.0000.011
normalize0.1240.0000.124
plot_CV_distr0.6650.0080.673
plot_PCA0.7230.0200.743
plot_PVCA15.288 0.09615.385
plot_PVCA.df15.220 0.06415.284
plot_corr_matrix0.0370.0000.037
plot_heatmap_diagnostic1.9530.0792.034
plot_heatmap_generic0.5910.0120.603
plot_hierarchical_clustering0.4100.0010.410
plot_peptide_corr_distribution1.2610.0041.266
plot_protein_corrplot0.2860.0110.298
plot_sample_corr_distribution1.2230.0131.236
plot_sample_corr_heatmap0.4670.0070.475
plot_sample_mean_or_boxplot3.4990.1203.619
prepare_PVCA_df15.168 0.09615.263
sample_annotation_to_colors0.0580.0010.058
transform_raw_data0.0090.0000.008