Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-04-12 11:05:51 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 scTensor on palomino4


To the developers/maintainers of the scTensor package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scTensor.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1824/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 2.8.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/scTensor
git_branch: RELEASE_3_16
git_last_commit: 4ead911
git_last_commit_date: 2022-11-01 11:18:55 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scTensor
Version: 2.8.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scTensor.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings scTensor_2.8.0.tar.gz
StartedAt: 2023-04-11 05:49:49 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 05:55:54 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 365.6 seconds
RetCode: 0
Status:   OK  
CheckDir: scTensor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scTensor.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings scTensor_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/scTensor.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.8.0'
* 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 '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
.simulateDropoutCounts: no visible binding for global variable 'v'
.simulateDropoutCounts: no visible binding for global variable 'm'
Undefined global functions or variables:
  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
  'F:/biocbuild/bbs-3.16-bioc/meat/scTensor.Rcheck/00check.log'
for details.



Installation output

scTensor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL scTensor
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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("scTensor")

> 
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_GermMale.R")

══ Testing test_GermMale.R ═════════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

── Failure ('test_GermMale.R:5:1'): (code run outside of `test_that()`) ────────
dim(GermMale) not equivalent to c(2547, 852).
1/2 mismatches
[1] 242 - 2547 == -2305


[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
> test_file("testthat/test_tsneGermMale.R")

══ Testing test_tsneGermMale.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 ] Done!
> test_file("testthat/test_labelGermMale.R")

══ Testing test_labelGermMale.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 ] Done!
> test_file("testthat/test_cellCellFunctions.R")

══ Testing test_cellCellFunctions.R ════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

── Error ('test_cellCellFunctions.R:4:1'): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `library(LRBase.Hsa.eg.db)`: there is no package called 'LRBase.Hsa.eg.db'
Backtrace:
 1. base::library(LRBase.Hsa.eg.db)
      at test_cellCellFunctions.R:4:0


[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
> test_file("testthat/test_CCSParamsFunctions.R")

══ Testing test_CCSParamsFunctions.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 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] Done!
> 
> proc.time()
   user  system elapsed 
  18.15    1.68   19.84 

Example timings

scTensor.Rcheck/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.010.000.01
cellCellDecomp000
cellCellRanks000
cellCellReport000
cellCellSetting0.010.000.01
cellCellSimulate000
getParam000
labelGermMale000
m0.000.020.02
newCCSParams000
scTensor-package000
setParam000
tsneGermMale0.000.010.01
v000