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CHECK report for scTensor on tokay2

This page was generated on 2019-10-16 12:42:57 -0400 (Wed, 16 Oct 2019).

Package 1481/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 1.0.13
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scTensor
Version: 1.0.13
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scTensor.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scTensor_1.0.13.tar.gz
StartedAt: 2019-10-16 06:58:33 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:08:50 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 616.5 seconds
RetCode: 0
Status:  OK  
CheckDir: scTensor.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scTensor.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scTensor_1.0.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scTensor.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '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 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
.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 ...
** 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-3.9-bioc/meat/scTensor.Rcheck/00check.log'
for details.

Installation output

scTensor.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scTensor_1.0.13.tar.gz && rm -rf scTensor.buildbin-libdir && mkdir scTensor.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scTensor.buildbin-libdir scTensor_1.0.13.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scTensor_1.0.13.zip && rm scTensor_1.0.13.tar.gz scTensor_1.0.13.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
100 7512k  100 7512k    0     0  51.4M      0 --:--:-- --:--:-- --:--:-- 54.3M

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_1.0.13.zip
* DONE (scTensor)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scTensor' successfully unpacked and MD5 sums checked

Tests output

scTensor.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
v |  OK F W S | Context

/ |   0       | GermMale
x |   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")
v |  OK F W S | Context

/ |   0       | tsneGermMale
v |   1       | tsneGermMale

== Results =====================================================================
OK:       1
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_labelGermMale.R")
v |  OK F W S | Context

/ |   0       | labelGermMale
v |   1       | labelGermMale

== Results =====================================================================
OK:       1
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_cellCellFunctions.R")
v |  OK F W S | Context

/ |   0       | cellCellFunctions
- |   1       | cellCellFunctions
- |   3 2     | cellCellFunctions
x |   3 3     | cellCellFunctions [1.1 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: 1.1 s

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

/ |   0       | CCSParamsFunctions
v |  11       | CCSParamsFunctions

== Results =====================================================================
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_convertToNCBIGeneID.R")
v |  OK F W S | Context

/ |   0       | convertToNCBIGeneID
v |   4       | convertToNCBIGeneID

== Results =====================================================================
OK:       4
Failed:   0
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
  23.10    2.53   25.71

scTensor.Rcheck/tests_x64/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-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")
v |  OK F W S | Context

/ |   0       | GermMale
x |   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: 0.2 s

OK:       0
Failed:   1
Warnings: 0
Skipped:  0
> test_file("testthat/test_tsneGermMale.R")
v |  OK F W S | Context

/ |   0       | tsneGermMale
v |   1       | tsneGermMale

== Results =====================================================================
OK:       1
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_labelGermMale.R")
v |  OK F W S | Context

/ |   0       | labelGermMale
v |   1       | labelGermMale

== Results =====================================================================
OK:       1
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_cellCellFunctions.R")
v |  OK F W S | Context

/ |   0       | cellCellFunctions
- |   1       | cellCellFunctions
x |   3 3     | cellCellFunctions [1.1 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: 1.1 s

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

/ |   0       | CCSParamsFunctions
v |  11       | CCSParamsFunctions

== Results =====================================================================
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
> test_file("testthat/test_convertToNCBIGeneID.R")
v |  OK F W S | Context

/ |   0       | convertToNCBIGeneID
v |   4       | convertToNCBIGeneID

== Results =====================================================================
OK:       4
Failed:   0
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
  23.67    1.14   24.79

Example timings

scTensor.Rcheck/examples_i386/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.010.000.02
cellCellDecomp0.020.000.01
cellCellRanks000
cellCellReport000
cellCellSetting000
cellCellSimulate000
convertToNCBIGeneID000
getParam0.020.000.01
labelGermMale000
m0.010.000.02
newCCSParams000
scTensor-package000
setParam000
tsneGermMale0.000.010.02
v000

scTensor.Rcheck/examples_x64/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.010.000.02
cellCellDecomp000
cellCellRanks000
cellCellReport000
cellCellSetting000
cellCellSimulate000
convertToNCBIGeneID000
getParam000
labelGermMale000
m000
newCCSParams000
scTensor-package0.020.000.01
setParam000
tsneGermMale000
v000