Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-30 13:55:13 -0500 (Tue, 30 Nov 2021).

CHECK results for scPCA on riesling1

To the developers/maintainers of the scPCA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scPCA.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 1726/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPCA 1.9.0  (landing page)
Philippe Boileau
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/scPCA
git_branch: master
git_last_commit: 0b0db46
git_last_commit_date: 2021-10-26 12:55:42 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scPCA
Version: 1.9.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scPCA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scPCA_1.9.0.tar.gz
StartedAt: 2021-11-30 03:51:26 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 03:57:16 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 350.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scPCA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scPCA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scPCA_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scPCA.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scPCA/DESCRIPTION' ... OK
* this is package 'scPCA' version '1.9.0'
* 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 'scPCA' 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
Namespaces in Imports field not imported from:
  'DelayedArray' 'matrixStats'
  All declared Imports should be used.
* 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
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/scPCA.Rcheck/00check.log'
for details.



Installation output

scPCA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/scPCA_1.9.0.tar.gz && rm -rf scPCA.buildbin-libdir && mkdir scPCA.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scPCA.buildbin-libdir scPCA_1.9.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scPCA_1.9.0.zip && rm scPCA_1.9.0.tar.gz scPCA_1.9.0.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
 37 1767k   37  665k    0     0  1823k      0 --:--:-- --:--:-- --:--:-- 1818k
100 1767k  100 1767k    0     0  4025k      0 --:--:-- --:--:-- --:--:-- 4016k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'scPCA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: scPCA
*** installing help indices
  converting help for package 'scPCA'
    finding HTML links ... done
    background_df                           html  
    bpContrastiveCov                        html  
    bpFitCPCA                               html  
    bpFitGrid                               html  
    checkArgs                               html  
    contrastiveCov                          html  
    covMat                                  html  
    cvSelectParams                          html  
    fitCPCA                                 html  
    fitGrid                                 html  
    safeColScale                            html  
    scPCA                                   html  
    selectParams                            html  
    spcaWrapper                             html  
    toy_df                                  html  
*** copying figures
** 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
* MD5 sums
packaged installation of 'scPCA' as scPCA_1.9.0.zip
* DONE (scPCA)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'scPCA' successfully unpacked and MD5 sums checked

Tests output

scPCA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(scPCA)
> 
> test_check("scPCA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 367 ]
> 
> proc.time()
   user  system elapsed 
  24.90    0.68   25.57 

Example timings

scPCA.Rcheck/scPCA-Ex.timings

nameusersystemelapsed
background_df000
scPCA1.260.041.31
toy_df000