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CHECK report for crisprseekplus on tokay1

This page was generated on 2019-04-13 11:27:15 -0400 (Sat, 13 Apr 2019).

Package 345/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprseekplus 1.8.0
Alper Kucukural
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/crisprseekplus
Branch: RELEASE_3_8
Last Commit: 17b4034
Last Changed Date: 2018-10-30 11:42:03 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: crisprseekplus
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crisprseekplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings crisprseekplus_1.8.0.tar.gz
StartedAt: 2019-04-13 01:33:53 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:40:29 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 395.9 seconds
RetCode: 0
Status:  OK  
CheckDir: crisprseekplus.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crisprseekplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings crisprseekplus_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/crisprseekplus.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crisprseekplus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crisprseekplus' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'crisprseekplus' 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
installpack: no visible global function definition for
  'install.packages'
Undefined global functions or variables:
  install.packages
Consider adding
  importFrom("utils", "install.packages")
to your NAMESPACE file.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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 'test-ui.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-ui.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-3.8-bioc/meat/crisprseekplus.Rcheck/00check.log'
for details.

Installation output

crisprseekplus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/crisprseekplus_1.8.0.tar.gz && rm -rf crisprseekplus.buildbin-libdir && mkdir crisprseekplus.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crisprseekplus.buildbin-libdir crisprseekplus_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL crisprseekplus_1.8.0.zip && rm crisprseekplus_1.8.0.tar.gz crisprseekplus_1.8.0.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
100  128k  100  128k    0     0  3902k      0 --:--:-- --:--:-- --:--:-- 4420k

install for i386

* installing *source* package 'crisprseekplus' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'crisprseekplus'
    finding HTML links ... done
    cspServer                               html  
    cspUI                                   html  
    disableDownload                         html  
    fileInputFunc                           html  
    getLoadingMsg                           html  
    getLogo                                 html  
    installpack                             html  
    startcrisprseekplus                     html  
    trueFalseFunc                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'crisprseekplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crisprseekplus' as crisprseekplus_1.8.0.zip
* DONE (crisprseekplus)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'crisprseekplus' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

crisprseekplus.Rcheck/tests_i386/test-ui.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> require(shiny)
Loading required package: shiny
> library(crisprseekplus)
Loading required package: shinyjs

Attaching package: 'shinyjs'

The following object is masked from 'package:shiny':

    runExample

The following objects are masked from 'package:methods':

    removeClass, show

Loading required package: CRISPRseek
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


> library(shinyjs)
> library(testthat)
> 
> test_that("trueFalseFunction works as expected", {
+     expect_false(trueFalseFunc(2))
+     expect_true(trueFalseFunc(1))
+     expect_silent(trueFalseFunc(3))
+   })
> 
> exampleFile <- system.file("extdata","gRNA.fa", package = "GUIDEseq")
> 
> test_that("tests fileInputFunction responds correctly to
+           a given input file/ receiving no input", {
+     expect_null(fileInputFunc(NULL, NULL))
+     })
> 
> test_that("Tests getLogo displays logo", {
+     expect_silent(goLogo <- getLogo())
+     expect_true(exists("goLogo"))
+     expect_equal(goLogo[[1]][[1]], "img")})
> 
> 
> 
> proc.time()
   user  system elapsed 
  10.56    1.23   11.79

crisprseekplus.Rcheck/tests_x64/test-ui.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> require(shiny)
Loading required package: shiny
> library(crisprseekplus)
Loading required package: shinyjs

Attaching package: 'shinyjs'

The following object is masked from 'package:shiny':

    runExample

The following objects are masked from 'package:methods':

    removeClass, show

Loading required package: CRISPRseek
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


> library(shinyjs)
> library(testthat)
> 
> test_that("trueFalseFunction works as expected", {
+     expect_false(trueFalseFunc(2))
+     expect_true(trueFalseFunc(1))
+     expect_silent(trueFalseFunc(3))
+   })
> 
> exampleFile <- system.file("extdata","gRNA.fa", package = "GUIDEseq")
> 
> test_that("tests fileInputFunction responds correctly to
+           a given input file/ receiving no input", {
+     expect_null(fileInputFunc(NULL, NULL))
+     })
> 
> test_that("Tests getLogo displays logo", {
+     expect_silent(goLogo <- getLogo())
+     expect_true(exists("goLogo"))
+     expect_equal(goLogo[[1]][[1]], "img")})
> 
> 
> 
> proc.time()
   user  system elapsed 
  10.95    0.57   11.53

Example timings

crisprseekplus.Rcheck/examples_i386/crisprseekplus-Ex.timings

nameusersystemelapsed
cspServer000
cspUI0.160.060.22
disableDownload000
fileInputFunc000
getLoadingMsg0.030.000.03
getLogo000
installpack000
startcrisprseekplus000
trueFalseFunc000

crisprseekplus.Rcheck/examples_x64/crisprseekplus-Ex.timings

nameusersystemelapsed
cspServer0.010.000.01
cspUI0.140.090.24
disableDownload000
fileInputFunc000
getLoadingMsg000
getLogo000
installpack000
startcrisprseekplus000
trueFalseFunc000