Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:23 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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 402/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
corral 1.4.0  (landing page)
Lauren Hsu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/corral
git_branch: RELEASE_3_14
git_last_commit: fcef936
git_last_commit_date: 2021-10-26 13:00:34 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: corral
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:corral.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings corral_1.4.0.tar.gz
StartedAt: 2022-04-12 17:56:18 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:02:58 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 400.5 seconds
RetCode: 0
Status:   OK  
CheckDir: corral.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:corral.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings corral_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/corral.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'corral/DESCRIPTION' ... OK
* this is package 'corral' version '1.4.0'
* 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
* 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
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
plot_embedding: no visible binding for global variable 'Xdim'
plot_embedding: no visible binding for global variable 'Ydim'
Undefined global functions or variables:
  Xdim Ydim
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
add_embeddings2scelist 21.70   2.75   25.65
corralm                22.03   1.90   24.57
corral                 21.22   1.88   23.70
plot_embedding_sce     12.35   1.02   13.67
sce2matlist            11.21   1.19   12.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
add_embeddings2scelist 22.44   2.13   25.70
corralm                17.94   1.81   20.39
corral                 17.50   2.09   20.23
sce2matlist             9.14   1.17   10.60
plot_embedding_sce      9.09   0.89   10.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/corral.Rcheck/00check.log'
for details.

Installation output

corral.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/corral_1.4.0.tar.gz && rm -rf corral.buildbin-libdir && mkdir corral.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=corral.buildbin-libdir corral_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL corral_1.4.0.zip && rm corral_1.4.0.tar.gz corral_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 12  362k   12 47039    0     0   296k      0  0:00:01 --:--:--  0:00:01  296k
100  362k  100  362k    0     0   873k      0 --:--:-- --:--:-- --:--:--  873k

install for i386

* installing *source* package 'corral' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'corral'
    finding HTML links ... done
    add_embeddings2scelist                  html  
    all_are                                 html  
    compsvd                                 html  
    corral                                  html  
    finding level-2 HTML links ... done

    corral_preproc                          html  
    corralm                                 html  
    earthmover_dist                         html  
    get_pct_var_exp_svd                     html  
    get_weights                             html  
    list2mat                                html  
    na2zero                                 html  
    obs2probs                               html  
    pairwise_rv                             html  
    plot_embedding                          html  
    plot_embedding_sce                      html  
    rv                                      html  
    sce2matlist                             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 'corral' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'corral' as corral_1.4.0.zip
* DONE (corral)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'corral' successfully unpacked and MD5 sums checked

Tests output

corral.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> 
> proc.time()
   user  system elapsed 
   0.25    0.04    0.28

corral.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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 
   0.25    0.07    0.29

Example timings

corral.Rcheck/examples_i386/corral-Ex.timings

nameusersystemelapsed
add_embeddings2scelist21.70 2.7525.65
all_are000
compsvd0.030.010.05
corral21.22 1.8823.70
corral_preproc0.020.000.02
corralm22.03 1.9024.57
earthmover_dist0.020.000.01
get_pct_var_exp_svd0.010.000.02
get_weights000
list2mat000
na2zero0.020.020.03
pairwise_rv000
plot_embedding0.700.010.77
plot_embedding_sce12.35 1.0213.67
rv000
sce2matlist11.21 1.1912.73

corral.Rcheck/examples_x64/corral-Ex.timings

nameusersystemelapsed
add_embeddings2scelist22.44 2.1325.70
all_are000
compsvd0.000.020.02
corral17.50 2.0920.23
corral_preproc0.010.000.01
corralm17.94 1.8120.39
earthmover_dist0.010.020.03
get_pct_var_exp_svd000
get_weights000
list2mat000
na2zero0.040.000.03
pairwise_rv000
plot_embedding0.640.000.65
plot_embedding_sce 9.09 0.8910.32
rv000
sce2matlist 9.14 1.1710.60