Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:19 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 corral on palomino3


To the developers/maintainers of the corral package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/corral.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 415/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
corral 1.6.0  (landing page)
Lauren Hsu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/corral
git_branch: RELEASE_3_15
git_last_commit: 9798002
git_last_commit_date: 2022-04-26 12:06:10 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: corral
Version: 1.6.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:corral.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings corral_1.6.0.tar.gz
StartedAt: 2022-10-18 23:16:00 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:21:03 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 303.2 seconds
RetCode: 0
Status:   OK  
CheckDir: corral.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:corral.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings corral_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/corral.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'corral/DESCRIPTION' ... OK
* this is package 'corral' version '1.6.0'
* 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 'corral' 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
Unexported object imported by a ':::' call: 'ggthemes:::check_pal_n'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biplot_corral: no visible binding for global variable 'Name'
plot_embedding: no visible binding for global variable 'Xdim'
plot_embedding: no visible binding for global variable 'Ydim'
scal_var: no visible binding for global variable 'PC_ind'
scal_var: no visible binding for global variable 'sv'
scal_var: no visible binding for global variable 'Batch'
Undefined global functions or variables:
  Batch Name PC_ind Xdim Ydim sv
* checking Rd files ... NOTE
prepare_Rd: corral_preproc.Rd:41-43: Dropping empty section \details
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
biplot_corral          58.64   2.00   60.78
add_embeddings2scelist 19.50   2.24   22.01
corralm                10.96   0.92   11.97
corral                 11.10   0.66   11.86
plot_embedding_sce      6.38   0.39    6.82
sce2matlist             6.02   0.46    6.57
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/corral.Rcheck/00check.log'
for details.



Installation output

corral.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL corral
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'corral' ...
** using staged installation
** R
** 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 (corral)

Tests output

corral.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
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.

> 
> proc.time()
   user  system elapsed 
   0.21    0.07    0.23 

Example timings

corral.Rcheck/corral-Ex.timings

nameusersystemelapsed
add_embeddings2scelist19.50 2.2422.01
all_are000
biplot_corral58.64 2.0060.78
compsvd0.010.000.01
corral11.10 0.6611.86
corral_preproc0.010.000.02
corralm10.96 0.9211.97
earthmover_dist0.010.000.02
get_pct_var_exp_svd000
get_weights000
list2mat000
na2zero0.000.020.02
pairwise_rv0.020.000.01
plot_embedding0.540.030.58
plot_embedding_sce6.380.396.82
rv000
scal_var0.300.010.31
scal_var_mat0.010.000.01
sce2matlist6.020.466.57
trim_matdist0.090.000.09
var_stabilize000