Koki Tsuyuzaki
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/scTensor |
| Branch: RELEASE_3_9 |
| Last Commit: 1398bf5 |
| Last Changed Date: 2019-09-22 22:20:52 -0400 (Sun, 22 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:16:56 -0400 (Wed, 16 Oct 2019).
| Package 1481/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scTensor 1.0.13 Koki Tsuyuzaki
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scTensor |
| Version: 1.0.13 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scTensor_1.0.13.tar.gz |
| StartedAt: 2019-10-16 04:53:32 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:01:06 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 454.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scTensor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scTensor_1.0.13.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (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 ‘1.0.13’ * 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 .cellCellSetting: no visible global function definition for 'assay<-' .importAssays: no visible global function definition for 'assays' .simulateDropoutCounts: no visible binding for global variable 'v' .simulateDropoutCounts: no visible binding for global variable 'm' Undefined global functions or variables: assay<- assays 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck/00check.log’ for details.
scTensor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scTensor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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)
scTensor.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
✔ | OK F W S | Context
⠏ | 0 | GermMale
✖ | 0 1 | GermMale
────────────────────────────────────────────────────────────────────────────────
test_GermMale.R:5: failure: (unknown)
dim(GermMale) not equivalent to c(2547, 852).
1/2 mismatches
[1] 242 - 2547 == -2305
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 0.1 s
OK: 0
Failed: 1
Warnings: 0
Skipped: 0
> test_file("testthat/test_tsneGermMale.R")
✔ | OK F W S | Context
⠏ | 0 | tsneGermMale
✔ | 1 | tsneGermMale
══ Results ═════════════════════════════════════════════════════════════════════
OK: 1
Failed: 0
Warnings: 0
Skipped: 0
> test_file("testthat/test_labelGermMale.R")
✔ | OK F W S | Context
⠏ | 0 | labelGermMale
✔ | 1 | labelGermMale
══ Results ═════════════════════════════════════════════════════════════════════
OK: 1
Failed: 0
Warnings: 0
Skipped: 0
> test_file("testthat/test_cellCellFunctions.R")
✔ | OK F W S | Context
⠏ | 0 | cellCellFunctions
⠋ | 1 | cellCellFunctions
✖ | 3 3 | cellCellFunctions [1.0 s]
────────────────────────────────────────────────────────────────────────────────
test_cellCellFunctions.R:21: failure: (unknown)
is.null(metadata(sce)$lrbase) isn't false.
test_cellCellFunctions.R:22: failure: (unknown)
is.null(metadata(sce)$color) isn't false.
test_cellCellFunctions.R:23: failure: (unknown)
is.null(metadata(sce)$label) isn't false.
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.0 s
OK: 3
Failed: 3
Warnings: 0
Skipped: 0
> test_file("testthat/test_CCSParamsFunctions.R")
✔ | OK F W S | Context
⠏ | 0 | CCSParamsFunctions
✔ | 11 | CCSParamsFunctions
══ Results ═════════════════════════════════════════════════════════════════════
OK: 11
Failed: 0
Warnings: 0
Skipped: 0
> test_file("testthat/test_convertToNCBIGeneID.R")
✔ | OK F W S | Context
⠏ | 0 | convertToNCBIGeneID
✔ | 4 | convertToNCBIGeneID
══ Results ═════════════════════════════════════════════════════════════════════
OK: 4
Failed: 0
Warnings: 0
Skipped: 0
Nice code.
>
> proc.time()
user system elapsed
21.002 0.949 22.438
scTensor.Rcheck/scTensor-Ex.timings
| name | user | system | elapsed | |
| GermMale | 0.008 | 0.004 | 0.012 | |
| cellCellDecomp | 0.002 | 0.000 | 0.002 | |
| cellCellRanks | 0.001 | 0.000 | 0.002 | |
| cellCellReport | 0.003 | 0.000 | 0.003 | |
| cellCellSetting | 0.001 | 0.000 | 0.001 | |
| cellCellSimulate | 0 | 0 | 0 | |
| convertToNCBIGeneID | 0.002 | 0.000 | 0.002 | |
| getParam | 0.002 | 0.000 | 0.001 | |
| labelGermMale | 0.002 | 0.000 | 0.002 | |
| m | 0.002 | 0.000 | 0.001 | |
| newCCSParams | 0 | 0 | 0 | |
| scTensor-package | 0.000 | 0.001 | 0.002 | |
| setParam | 0.000 | 0.001 | 0.002 | |
| tsneGermMale | 0.001 | 0.000 | 0.002 | |
| v | 0.002 | 0.000 | 0.002 | |