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CHECK report for scTensor on malbec2

This page was generated on 2019-04-09 11:52:21 -0400 (Tue, 09 Apr 2019).

Package 1451/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 0.99.22
Koki Tsuyuzaki
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/scTensor
Branch: master
Last Commit: feb6b7d
Last Changed Date: 2019-01-02 04:07:13 -0400 (Wed, 02 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: scTensor
Version: 0.99.22
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_0.99.22.tar.gz
StartedAt: 2019-04-09 03:31:47 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:39:16 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 449.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: scTensor.Rcheck
Warnings: 1

Command output

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### 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_0.99.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘0.99.22’
* 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 ... 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 ... WARNING
Output for data("m", package = "scTensor"):
  No dataset created in 'envir'
Output for data("v", package = "scTensor"):
  No dataset created in 'envir'
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck/00check.log’
for details.



Installation output

scTensor.Rcheck/00install.out

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###
### 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)

Tests output

scTensor.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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
✖ |  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 ═════════════════════════════════════════════════════════════════════
OK:       0
Failed:   1
Warnings: 0
Skipped:  0
> test_file("testthat/test_tsneGermMale.R")
✔ | OK F W S | Context

⠏ |  0       | tsneGermMale
⠋ |  1       | 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
✔ |  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
⠙ |  2       | cellCellFunctions
⠹ |  3       | cellCellFunctions
⠸ |  3 1     | cellCellFunctions
⠼ |  3 2     | cellCellFunctions
⠴ |  3 3     | cellCellFunctions
✖ |  3 3     | cellCellFunctions [0.7 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: 0.7 s

OK:       3
Failed:   3
Warnings: 0
Skipped:  0
> test_file("testthat/test_CCSParamsFunctions.R")
✔ | OK F W S | Context

⠋ |  1       | 0
⠙ |  2       | 0
⠹ |  3       | 0
⠸ |  4       | 0
⠼ |  5       | 0
⠴ |  6       | 0
⠦ |  7       | 0
⠧ |  8       | 0
⠇ |  9       | 0
⠏ | 10       | 0
⠋ | 11       | 0
══ Results ═════════════════════════════════════════════════════════════════════
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 22.476   0.694  23.270 

Example timings

scTensor.Rcheck/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.0120.0000.012
cellCellDecomp0.0020.0000.002
cellCellRanks000
cellCellReport0.0010.0000.001
cellCellSetting0.0010.0000.001
cellCellSimulate0.0010.0000.001
getParam0.0010.0000.001
labelGermMale0.0010.0000.001
m0.0020.0000.002
newCCSParams000
scTensor-package0.0020.0000.002
setParam0.0010.0000.002
tsneGermMale0.0010.0000.001
v0.0000.0010.002