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CHECK report for scTensor on celaya2

This page was generated on 2019-10-16 13:03:52 -0400 (Wed, 16 Oct 2019).

Package 1481/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 1.0.13
Koki Tsuyuzaki
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/scTensor
Branch: RELEASE_3_9
Last Commit: 1398bf5
Last Changed Date: 2019-09-22 22:20:52 -0400 (Sun, 22 Sep 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: scTensor
Version: 1.0.13
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTensor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTensor_1.0.13.tar.gz
StartedAt: 2019-10-16 06:40:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:52:22 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 736.8 seconds
RetCode: 0
Status:  OK 
CheckDir: scTensor.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTensor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTensor_1.0.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scTensor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTensor’ version ‘1.0.13’
* 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 ‘scTensor’ 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 ... NOTE
.cellCellSetting: no visible global function definition for 'assay<-'
.importAssays: no visible global function definition for 'assays'
.simulateDropoutCounts: no visible binding for global variable 'v'
.simulateDropoutCounts: no visible binding for global variable 'm'
Undefined global functions or variables:
  assay<- assays m v
* 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
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck/00check.log’
for details.



Installation output

scTensor.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scTensor
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scTensor’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'show' in package 'scTensor'
** 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 (scTensor)

Tests output

scTensor.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("scTensor")


> 
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_GermMale.R")
✔ |  OK F W S | Context

⠏ |   0       | GermMale
✖ |   0 1     | GermMale
────────────────────────────────────────────────────────────────────────────────
test_GermMale.R:5: failure: (unknown)
dim(GermMale) not equivalent to c(2547, 852).
1/2 mismatches
[1] 242 - 2547 == -2305
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 0.2 s

OK:       0
Failed:   1
Warnings: 0
Skipped:  0
> test_file("testthat/test_tsneGermMale.R")
✔ |  OK F W S | Context

⠏ |   0       | tsneGermMale
✔ |   1       | tsneGermMale

══ Results ═════════════════════════════════════════════════════════════════════
OK:       1
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_labelGermMale.R")
✔ |  OK F W S | Context

⠏ |   0       | labelGermMale
✔ |   1       | labelGermMale

══ Results ═════════════════════════════════════════════════════════════════════
OK:       1
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_cellCellFunctions.R")
✔ |  OK F W S | Context

⠏ |   0       | cellCellFunctions
⠋ |   1       | cellCellFunctions
⠸ |   3 1     | cellCellFunctions
✖ |   3 3     | cellCellFunctions [1.5 s]
────────────────────────────────────────────────────────────────────────────────
test_cellCellFunctions.R:21: failure: (unknown)
is.null(metadata(sce)$lrbase) isn't false.

test_cellCellFunctions.R:22: failure: (unknown)
is.null(metadata(sce)$color) isn't false.

test_cellCellFunctions.R:23: failure: (unknown)
is.null(metadata(sce)$label) isn't false.
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.5 s

OK:       3
Failed:   3
Warnings: 0
Skipped:  0
> test_file("testthat/test_CCSParamsFunctions.R")
✔ |  OK F W S | Context

⠏ |   0       | CCSParamsFunctions
✔ |  11       | CCSParamsFunctions

══ Results ═════════════════════════════════════════════════════════════════════
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_convertToNCBIGeneID.R")
✔ |  OK F W S | Context

⠏ |   0       | convertToNCBIGeneID
✔ |   4       | convertToNCBIGeneID

══ Results ═════════════════════════════════════════════════════════════════════
OK:       4
Failed:   0
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 31.086   2.875  33.930 

Example timings

scTensor.Rcheck/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.0170.0050.022
cellCellDecomp0.0050.0010.005
cellCellRanks0.0020.0010.002
cellCellReport0.0100.0010.010
cellCellSetting0.0010.0000.002
cellCellSimulate0.0000.0010.001
convertToNCBIGeneID0.0020.0010.003
getParam0.0020.0010.003
labelGermMale0.0020.0010.003
m0.0030.0020.005
newCCSParams0.0010.0000.000
scTensor-package0.0050.0010.006
setParam0.0030.0010.004
tsneGermMale0.0010.0010.003
v0.0020.0010.003