Package: CrossICC

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrossICC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CrossICC_1.0.0.tar.gz

StartedAt: 2020-04-15 02:23:52 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:29:25 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 333.0 seconds

RetCode: 0

Status:  OK

CheckDir: CrossICC.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrossICC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CrossICC_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CrossICC.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CrossICC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrossICC' version '1.0.0'
* 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 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
* 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
.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
CrossICC        13.51   0.14   13.70
summaryCrossICC 11.42   0.11   11.53
ssGSEA          11.39   0.03   11.43
predictor       11.31   0.06   11.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
summaryCrossICC 17.92   0.08   17.97
predictor       17.04   0.09   17.14
ssGSEA          16.97   0.03   17.00
CrossICC        16.78   0.06   16.84
* 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-3.10-bioc/meat/CrossICC.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CrossICC_1.0.0.tar.gz && rm -rf CrossICC.buildbin-libdir && mkdir CrossICC.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrossICC.buildbin-libdir CrossICC_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CrossICC_1.0.0.zip && rm CrossICC_1.0.0.tar.gz CrossICC_1.0.0.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 2106k  100 2106k    0     0  4585k      0 --:--:-- --:--:-- --:--:-- 4618k

install for i386

* installing *source* package 'CrossICC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CrossICC'
    finding HTML links ... done
    Cal.ARI                                 html  
    CrossICC                                html  
    CrossICCInput                           html  
    centroidOfcentroid                      html  
    demo.platforms                          html  
    get_jarrad_index_df_fromDF              html  
    get_jarrad_index_df_fromlist            html  
    get_overlap_test_by_fisher              html  
    predictor                               html  
    rand.index                              html  
    ssGSEA                                  html  
    summaryCrossICC                         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 'CrossICC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrossICC' as CrossICC_1.0.0.zip
* DONE (CrossICC)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CrossICC' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(CrossICC)
Loading required package: MASS
> 
> test_check("CrossICC")
Wed Apr 15 02:27:12 2020 -- start iteration: 1 
352 genes were engaged in this iteration.
Wed Apr 15 02:27:24 2020 -- start iteration: 2 
349 genes were engaged in this iteration.
Wed Apr 15 02:27:38 2020 -- start iteration: 3 
346 genes were engaged in this iteration.
Wed Apr 15 02:27:50 2020 -- start iteration: 4 
345 genes were engaged in this iteration.
Wed Apr 15 02:28:05 2020 -- start iteration: 5 
345 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.
Wed Apr 15 02:28:20 2020 -- Iteration finished! Iteration time for reaching convergence/limit: 4 
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  70.51    0.59   71.10 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(CrossICC)
Loading required package: MASS
> 
> test_check("CrossICC")
Wed Apr 15 02:28:24 2020 -- start iteration: 1 
351 genes were engaged in this iteration.
Wed Apr 15 02:28:38 2020 -- start iteration: 2 
347 genes were engaged in this iteration.
Wed Apr 15 02:28:56 2020 -- start iteration: 3 
344 genes were engaged in this iteration.
Wed Apr 15 02:29:09 2020 -- start iteration: 4 
344 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.
Wed Apr 15 02:29:21 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 
  60.51    0.35   60.96