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CHECK report for scRecover on malbec1

This page was generated on 2020-04-15 12:15:36 -0400 (Wed, 15 Apr 2020).

Package 1546/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scRecover 1.2.0
Zhun Miao
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/scRecover
Branch: RELEASE_3_10
Last Commit: 1498e40
Last Changed Date: 2019-10-29 13:11:38 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scRecover
Version: 1.2.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scRecover.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scRecover_1.2.0.tar.gz
StartedAt: 2020-04-15 06:28:45 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:31:24 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 158.7 seconds
RetCode: 0
Status:  OK 
CheckDir: scRecover.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scRecover.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scRecover_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/scRecover.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRecover/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scRecover’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scRecover’ 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: ‘foreach:::.foreachGlobals’
  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
estDropoutNum: no visible global function definition for ‘counts’
Undefined global functions or variables:
  counts
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
scRecover 31.284  0.216  50.362
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/scRecover.Rcheck/00check.log’
for details.



Installation output

scRecover.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scRecover
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘scRecover’ ...
** using staged installation
** R
** data
** 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 (scRecover)

Tests output

scRecover.Rcheck/tests/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-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(scRecover)
> 
> test_check("scRecover")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 28 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.660   2.520  10.822 

Example timings

scRecover.Rcheck/scRecover-Ex.timings

nameusersystemelapsed
countsSampling0.0400.0120.050
estDropoutNum0.1200.0120.132
normalization0.9600.0080.972
scRecover31.284 0.21650.362
scRecoverTest0.0160.0000.017