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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1908/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 2.16.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/scTensor
git_branch: RELEASE_3_20
git_last_commit: a87f346
git_last_commit_date: 2024-10-29 10:33:22 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for scTensor on kunpeng2

To the developers/maintainers of the scTensor package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: scTensor
Version: 2.16.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scTensor_2.16.0.tar.gz
StartedAt: 2024-11-20 12:18:38 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 12:26:00 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 441.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scTensor.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scTensor_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scTensor.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scTensor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTensor’ version ‘2.16.0’
* 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 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘AnnotationHub’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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 ... WARNING
checkRd: (5) newCCSParams.Rd:8: \item in \arguments must have non-empty label
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scTensor.Rcheck/00check.log’
for details.


Installation output

scTensor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scTensor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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:4:1

[ 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 
 20.283   1.660  21.562 

Example timings

scTensor.Rcheck/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.0070.0040.010
cellCellDecomp0.0040.0000.004
cellCellRanks0.0000.0010.001
cellCellReport0.0020.0020.004
cellCellSetting0.0010.0000.001
cellCellSimulate0.0010.0000.001
getParam0.0010.0000.001
labelGermMale0.0020.0000.001
m0.0030.0000.002
newCCSParams000
scTensor-package000
setParam0.0020.0000.003
tsneGermMale0.0010.0000.002
v0.0020.0000.001