Koki Tsuyuzaki
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/scTensor |
| git_branch: RELEASE_3_13 |
| git_last_commit: adb0ecb |
| git_last_commit_date: 2021-05-19 12:39:42 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1718/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scTensor 2.2.0 (landing page) Koki Tsuyuzaki
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: scTensor |
| Version: 2.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scTensor.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scTensor_2.2.0.tar.gz |
| StartedAt: 2021-10-15 05:24:34 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:35:41 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 666.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scTensor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scTensor.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scTensor_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scTensor.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'scTensor/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scTensor' version '2.2.0' * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scTensor.Rcheck/00check.log' for details.
scTensor.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/scTensor_2.2.0.tar.gz && rm -rf scTensor.buildbin-libdir && mkdir scTensor.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scTensor.buildbin-libdir scTensor_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scTensor_2.2.0.zip && rm scTensor_2.2.0.tar.gz scTensor_2.2.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
9 10.7M 9 1065k 0 0 1656k 0 0:00:06 --:--:-- 0:00:06 1656k
24 10.7M 24 2732k 0 0 1475k 0 0:00:07 0:00:01 0:00:06 1475k
43 10.7M 43 4822k 0 0 1810k 0 0:00:06 0:00:02 0:00:04 1810k
80 10.7M 80 8840k 0 0 2412k 0 0:00:04 0:00:03 0:00:01 2412k
100 10.7M 100 10.7M 0 0 2673k 0 0:00:04 0:00:04 --:--:-- 2674k
install for i386
* 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
converting help for package 'scTensor'
finding HTML links ... done
CCSParams-class html
GermMale html
cellCellDecomp html
cellCellRanks html
cellCellReport html
cellCellSetting html
cellCellSimulate html
convertToNCBIGeneID html
getParam html
labelGermMale html
m html
newCCSParams html
scTensor-package html
setParam html
tsneGermMale html
v html
** 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
install for x64
* installing *source* package 'scTensor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scTensor' as scTensor_2.2.0.zip
* DONE (scTensor)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'scTensor' successfully unpacked and MD5 sums checked
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scTensor.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 0 | WARN 1 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 3 ]
-- Warning (test_cellCellFunctions.R:4:1): (code run outside of `test_that()`) --
Package 'LRBase.Hsa.eg.db' is deprecated and will be removed from
Bioconductor version 3.14. For details, check the vignette of
'AHLRBaseDbs'.
Backtrace:
1. base::library(LRBase.Hsa.eg.db) test_cellCellFunctions.R:4:0
6. base::attachNamespace(ns, pos = pos, deps, exclude, include.only)
7. base:::runHook(".onAttach", ns, dirname(nspath), nsname)
12. LRBase.Hsa.eg.db:::fun(libname, pkgname)
13. base::.Deprecated(msg = paste(strwrap(msg, exdent = 2), collapse = "\n"))
-- Failure (test_cellCellFunctions.R:21:1): (code run outside of `test_that()`) --
is.null(metadata(sce)$lrbase) is not FALSE
`actual`: TRUE
`expected`: FALSE
-- Failure (test_cellCellFunctions.R:22:1): (code run outside of `test_that()`) --
is.null(metadata(sce)$color) is not FALSE
`actual`: TRUE
`expected`: FALSE
-- Failure (test_cellCellFunctions.R:23:1): (code run outside of `test_that()`) --
is.null(metadata(sce)$label) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 3 ]
> 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
24.07 3.32 27.53
|
scTensor.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 0 | WARN 1 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 3 ]
-- Warning (test_cellCellFunctions.R:4:1): (code run outside of `test_that()`) --
Package 'LRBase.Hsa.eg.db' is deprecated and will be removed from
Bioconductor version 3.14. For details, check the vignette of
'AHLRBaseDbs'.
Backtrace:
1. base::library(LRBase.Hsa.eg.db) test_cellCellFunctions.R:4:0
6. base::attachNamespace(ns, pos = pos, deps, exclude, include.only)
7. base:::runHook(".onAttach", ns, dirname(nspath), nsname)
12. LRBase.Hsa.eg.db:::fun(libname, pkgname)
13. base::.Deprecated(msg = paste(strwrap(msg, exdent = 2), collapse = "\n"))
-- Failure (test_cellCellFunctions.R:21:1): (code run outside of `test_that()`) --
is.null(metadata(sce)$lrbase) is not FALSE
`actual`: TRUE
`expected`: FALSE
-- Failure (test_cellCellFunctions.R:22:1): (code run outside of `test_that()`) --
is.null(metadata(sce)$color) is not FALSE
`actual`: TRUE
`expected`: FALSE
-- Failure (test_cellCellFunctions.R:23:1): (code run outside of `test_that()`) --
is.null(metadata(sce)$label) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 3 ]
> 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
24.31 1.54 25.84
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scTensor.Rcheck/examples_i386/scTensor-Ex.timings
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scTensor.Rcheck/examples_x64/scTensor-Ex.timings
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