Back to Build/check report for BioC 3.17
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-01-02 09:00:50 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 scTGIF on palomino5


To the developers/maintainers of the scTGIF package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1805/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTGIF 1.13.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/scTGIF
git_branch: master
git_last_commit: fbd870b
git_last_commit_date: 2022-11-01 11:20:56 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: scTGIF
Version: 1.13.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scTGIF.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scTGIF_1.13.0.tar.gz
StartedAt: 2022-12-29 03:24:19 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 03:28:05 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 225.8 seconds
RetCode: 0
Status:   OK  
CheckDir: scTGIF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scTGIF.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scTGIF_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/scTGIF.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scTGIF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scTGIF' version '1.13.0'
* 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 '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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/scTGIF.Rcheck/00check.log'
for details.

Installation output

scTGIF.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL scTGIF
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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.

> library("testthat")
> library("scTGIF")
> 
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_DistalLungEpithelium.R")

══ Testing test_DistalLungEpithelium.R ═════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] Done!
> test_file("testthat/test_TGIFFunctions.R")

══ Testing test_TGIFFunctions.R ════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] Done!
> test_file("testthat/test_convertRowID.R")

══ Testing test_convertRowID.R ═════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |======================================================================| 100%

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |======================================================================| 100%

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 5 ]
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 5 ]
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 5 ]
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 6 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 6 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 7 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%

[ FAIL 3 | WARN 3 | SKIP 0 | PASS 8 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%

[ FAIL 3 | WARN 3 | SKIP 0 | PASS 9 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 10 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 11 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 12 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |======================================================================| 100%

[ FAIL 4 | WARN 3 | SKIP 0 | PASS 12 ]
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |======================================================================| 100%

[ FAIL 5 | WARN 3 | SKIP 0 | PASS 12 ]
[ FAIL 5 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 6 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 6 | WARN 5 | SKIP 0 | PASS 12 ]
[ FAIL 6 | WARN 5 | SKIP 0 | PASS 13 ]
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 13 ]
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 14 ]

── Failure ('test_convertRowID.R:48'): (code run outside of `test_that()`) ─────
identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Failure ('test_convertRowID.R:51'): (code run outside of `test_that()`) ─────
identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning ('test_convertRowID.R:53'): (code run outside of `test_that()`) ─────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.mean")
      at test_convertRowID.R:53:0
 2. scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Failure ('test_convertRowID.R:54'): (code run outside of `test_that()`) ─────
identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning ('test_convertRowID.R:56'): (code run outside of `test_that()`) ─────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.var")
      at test_convertRowID.R:56:0
 2. scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Warning ('test_convertRowID.R:59'): (code run outside of `test_that()`) ─────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.cv2")
      at test_convertRowID.R:59:0
 2. scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Failure ('test_convertRowID.R:112'): (code run outside of `test_that()`) ────
identical(rownames(out$output), c("5", "2", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Failure ('test_convertRowID.R:115'): (code run outside of `test_that()`) ────
identical(rownames(out$output), c("5", "2", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning ('test_convertRowID.R:117'): (code run outside of `test_that()`) ────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.mean")
      at test_convertRowID.R:117:0
 2. scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Failure ('test_convertRowID.R:118'): (code run outside of `test_that()`) ────
identical(rownames(out$output), c("5", "2", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning ('test_convertRowID.R:120'): (code run outside of `test_that()`) ────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.var")
      at test_convertRowID.R:120:0
 2. scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Warning ('test_convertRowID.R:123'): (code run outside of `test_that()`) ────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.cv2")
      at test_convertRowID.R:123:0
 2. scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)


[ FAIL 6 | WARN 6 | SKIP 0 | PASS 14 ]
> test_file("testthat/test_cellMarkerToGmt.R")

══ Testing test_cellMarkerToGmt.R ══════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 5 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 6 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 9 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 10 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 13 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]

── Warning ('test_cellMarkerToGmt.R:134'): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Meniscus
Backtrace:
 1. GSEABase::getGmt(outfile2_1)
      at test_cellMarkerToGmt.R:134:0
 2. GSEABase:::.warningf(...)

── Warning ('test_cellMarkerToGmt.R:135'): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Meniscus
Backtrace:
 1. GSEABase::getGmt(outfile2_2)
      at test_cellMarkerToGmt.R:135:0
 2. GSEABase:::.warningf(...)

── Warning ('test_cellMarkerToGmt.R:140'): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Pancreas
Backtrace:
 1. GSEABase::getGmt(outfile3_1)
      at test_cellMarkerToGmt.R:140:0
 2. GSEABase:::.warningf(...)

── Warning ('test_cellMarkerToGmt.R:141'): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Pancreas
Backtrace:
 1. GSEABase::getGmt(outfile3_2)
      at test_cellMarkerToGmt.R:141:0
 2. GSEABase:::.warningf(...)


[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  12.06    1.23   13.40

Example timings

scTGIF.Rcheck/scTGIF-Ex.timings

nameusersystemelapsed
DistalLungEpithelium0.020.000.01
calcTGIF000
cellMarkerToGmt0.170.010.19
convertRowID0.030.000.03
label.DistalLungEpithelium000
pca.DistalLungEpithelium000
reportTGIF0.020.000.01
settingTGIF000