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CHECK report for scTGIF on machv2

This page was generated on 2020-10-17 11:59:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE scTGIF PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1615/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTGIF 1.2.2
Koki Tsuyuzaki
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/scTGIF
Branch: RELEASE_3_11
Last Commit: 2f7e6a2
Last Changed Date: 2020-07-16 03:31:38 -0400 (Thu, 16 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: scTGIF
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTGIF_1.2.2.tar.gz
StartedAt: 2020-10-17 05:09:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:16:08 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 407.7 seconds
RetCode: 0
Status:  OK 
CheckDir: scTGIF.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTGIF_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/scTGIF.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scTGIF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTGIF’ version ‘1.2.2’
* 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 ‘scTGIF’ 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: ‘schex:::.make_hexbin_function’
  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 ... 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 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-3.11-bioc/meat/scTGIF.Rcheck/00check.log’
for details.

Installation output

scTGIF.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘scTGIF’ ...
** 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 (scTGIF)

Tests output

scTGIF.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("scTGIF")
> 
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_DistalLungEpithelium.R")
✔ |  OK F W S | Context

⠏ |   0       | DistalLungEpithelium
✔ |   5       | DistalLungEpithelium

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 0.3 s

OK:       5
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_TGIFFunctions.R")
✔ |  OK F W S | Context

⠏ |   0       | TGIFFunctions
⠋ |   1       | TGIFFunctions
✔ |   3       | TGIFFunctions [1.1 s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.1 s

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

⠏ |   0       | convertRowID
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✖ |  14 6 6   | convertRowID [0.3 s]
────────────────────────────────────────────────────────────────────────────────
test_convertRowID.R:48: failure: (unknown)
identical(rownames(out$output), c("3", "2", "4", "7")) isn't true.

test_convertRowID.R:51: failure: (unknown)
identical(rownames(out$output), c("3", "2", "4", "7")) isn't true.

test_convertRowID.R:53: warning: (unknown)
number of items to replace is not a multiple of replacement length

test_convertRowID.R:54: failure: (unknown)
identical(rownames(out$output), c("3", "2", "4", "7")) isn't true.

test_convertRowID.R:56: warning: (unknown)
number of items to replace is not a multiple of replacement length

test_convertRowID.R:59: warning: (unknown)
number of items to replace is not a multiple of replacement length

test_convertRowID.R:112: failure: (unknown)
identical(rownames(out$output), c("5", "2", "7")) isn't true.

test_convertRowID.R:115: failure: (unknown)
identical(rownames(out$output), c("5", "2", "7")) isn't true.

test_convertRowID.R:117: warning: (unknown)
number of items to replace is not a multiple of replacement length

test_convertRowID.R:118: failure: (unknown)
identical(rownames(out$output), c("5", "2", "7")) isn't true.

test_convertRowID.R:120: warning: (unknown)
number of items to replace is not a multiple of replacement length

test_convertRowID.R:123: warning: (unknown)
number of items to replace is not a multiple of replacement length
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 0.3 s

OK:       14
Failed:   6
Warnings: 6
Skipped:  0
> test_file("testthat/test_cellMarkerToGmt.R")
✔ |  OK F W S | Context

⠏ |   0       | cellMarkerToGmt
⠋ |   0   1   | cellMarkerToGmt
⠼ |   1   4   | cellMarkerToGmt
✔ |  16   4   | cellMarkerToGmt [0.5 s]
────────────────────────────────────────────────────────────────────────────────
test_cellMarkerToGmt.R:134: warning: (unknown)
1 record(s) contain duplicate ids: Meniscus

test_cellMarkerToGmt.R:135: warning: (unknown)
1 record(s) contain duplicate ids: Meniscus

test_cellMarkerToGmt.R:140: warning: (unknown)
1 record(s) contain duplicate ids: Pancreas

test_cellMarkerToGmt.R:141: warning: (unknown)
1 record(s) contain duplicate ids: Pancreas
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 0.5 s

OK:       16
Failed:   0
Warnings: 4
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 21.032   2.503  22.678

Example timings

scTGIF.Rcheck/scTGIF-Ex.timings

nameusersystemelapsed
DistalLungEpithelium0.0460.0050.050
calcTGIF0.0190.0020.020
cellMarkerToGmt0.5480.0620.607
convertRowID0.2010.0200.221
label.DistalLungEpithelium0.0160.0030.019
pca.DistalLungEpithelium0.0170.0030.019
reportTGIF0.0340.0030.037
settingTGIF0.0110.0020.012