Package: CrossICC

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CrossICC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CrossICC_1.1.0.tar.gz

StartedAt: 2020-01-16 03:22:24 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:28:24 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 360.0 seconds

RetCode: 0

Status:  OK

CheckDir: CrossICC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CrossICC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CrossICC_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CrossICC.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CrossICC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CrossICC’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘CrossICC’ 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
.mergemodel: no visible global function definition for ‘coxph’
CrossICC: no visible global function definition for ‘.’
FAIME: no visible binding for global variable ‘SampleExp’
get.max.var.rows: no visible binding for global variable ‘V1’
predictor: no visible global function definition for ‘assay’
runFAIME: no visible global function definition for ‘assay’
Undefined global functions or variables:
  . SampleExp V1 assay coxph
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
predictor       26.891  3.718  30.541
ssGSEA          25.797  3.547  28.559
CrossICC        24.076  4.430  28.348
summaryCrossICC 23.903  3.944  28.017
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CrossICC.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CrossICC
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CrossICC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (CrossICC)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(CrossICC)
Loading required package: MASS
> 
> test_check("CrossICC")
Thu Jan 16 03:26:23 2020 -- start iteration: 1 
351 genes were engaged in this iteration.
Thu Jan 16 03:26:52 2020 -- start iteration: 2 
313 genes were engaged in this iteration.
Thu Jan 16 03:27:19 2020 -- start iteration: 3 
312 genes were engaged in this iteration.
Thu Jan 16 03:27:47 2020 -- start iteration: 4 
312 genes were engaged in this iteration.
A CrossICC.object.rds file will be generated in home directory by default.
      Note that the previous file will be overridden.
Thu Jan 16 03:28:15 2020 -- Iteration finished! Iteration time for reaching convergence/limit: 3 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
101.587  16.918 118.459 

name	user	system	elapsed
CrossICC	24.076	4.430	28.348
CrossICCInput	0.002	0.001	0.001
predictor	26.891	3.718	30.541
ssGSEA	25.797	3.547	28.559
summaryCrossICC	23.903	3.944	28.017