Koki Tsuyuzaki
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/scTensor |
| git_branch: RELEASE_3_17 |
| git_last_commit: 32e2912 |
| git_last_commit_date: 2023-04-25 11:06:25 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1865/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scTensor 2.10.0 (landing page) Koki Tsuyuzaki
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the scTensor package: - 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. |
| Package: scTensor |
| Version: 2.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scTensor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scTensor_2.10.0.tar.gz |
| StartedAt: 2023-10-18 23:32:12 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 23:45:10 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 778.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scTensor.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scTensor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scTensor_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scTensor.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scTensor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTensor’ version ‘2.10.0’
* 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 ... 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 ... 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 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scTensor.Rcheck/00check.log’
for details.
scTensor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scTensor ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)
scTensor.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
>
> 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
19.567 1.750 37.161
scTensor.Rcheck/scTensor-Ex.timings
| name | user | system | elapsed | |
| GermMale | 0.010 | 0.002 | 0.018 | |
| cellCellDecomp | 0.002 | 0.000 | 0.003 | |
| cellCellRanks | 0.001 | 0.000 | 0.002 | |
| cellCellReport | 0.007 | 0.001 | 0.012 | |
| cellCellSetting | 0.001 | 0.001 | 0.003 | |
| cellCellSimulate | 0.001 | 0.000 | 0.001 | |
| getParam | 0.002 | 0.000 | 0.005 | |
| labelGermMale | 0.002 | 0.001 | 0.004 | |
| m | 0.002 | 0.002 | 0.003 | |
| newCCSParams | 0 | 0 | 0 | |
| scTensor-package | 0 | 0 | 0 | |
| setParam | 0.002 | 0.001 | 0.005 | |
| tsneGermMale | 0.001 | 0.001 | 0.003 | |
| v | 0.002 | 0.001 | 0.005 | |