Package: SPONGE

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SPONGE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPONGE_1.4.0.tar.gz

StartedAt: 2019-04-16 02:57:13 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:02:25 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 312.7 seconds

RetCode: 0

Status:  OK

CheckDir: SPONGE.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:SPONGE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPONGE_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SPONGE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPONGE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPONGE’ version ‘1.4.0’
* 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 ‘SPONGE’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
* 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
checkLambda: no visible binding for global variable ‘i’
check_and_convert_expression_data: no visible global function
  definition for ‘attach.big.matrix’
check_and_convert_expression_data: no visible global function
  definition for ‘mwhich’
compute_p_values: no visible binding for global variable ‘cor_cut’
compute_p_values: no visible binding for global variable ‘df_cut’
compute_p_values: no visible global function definition for ‘J’
compute_p_values: no visible binding for global variable ‘.I’
compute_p_values: no visible binding for global variable ‘.EACHI’
compute_p_values: no visible binding for global variable ‘p.val’
compute_p_values: no visible global function definition for ‘:=’
compute_p_values: no visible binding for global variable ‘p.adj’
determine_cutoffs_for_null_model_partitioning: no visible global
  function definition for ‘:=’
determine_cutoffs_for_null_model_partitioning: no visible binding for
  global variable ‘cor_cut’
determine_cutoffs_for_null_model_partitioning: no visible binding for
  global variable ‘df_cut’
fn_elasticnet: no visible binding for global variable ‘alpha’
fn_gene_miRNA_F_test: no visible binding for global variable ‘mirna’
fn_get_model_coef: no visible binding for global variable ‘gene’
isplitDT2 : nextEl: no visible global function definition for ‘.’
processChunk: no visible binding for global variable ‘geneA_idx’
processChunk: no visible binding for global variable ‘geneB_idx’
processChunk: no visible binding for global variable ‘geneA’
processChunk: no visible binding for global variable ‘geneB’
processChunk: no visible binding for global variable ‘mirna’
sample_zero_mscor_cov: no visible binding for global variable
  ‘solution’
sample_zero_mscor_cov: no visible global function definition for ‘ginv’
sample_zero_mscor_cov: no visible binding for global variable ‘i’
sample_zero_mscor_data: no visible binding for global variable
  ‘cov.matrix’
sponge: no visible binding for global variable ‘i’
sponge: no visible global function definition for ‘attach.big.matrix’
sponge: no visible binding for global variable ‘gene_combis’
sponge_build_null_model: no visible binding for global variable
  ‘precomputed_cov_matrices’
sponge_build_null_model: no visible binding for global variable
  ‘cov.matrices.m’
sponge_build_null_model: no visible binding for global variable
  ‘cov.matrices.k’
sponge_build_null_model: no visible binding for global variable ‘m’
sponge_build_null_model: no visible binding for global variable ‘k’
sponge_compute_p_values: no visible binding for global variable ‘dt.m’
sponge_compute_p_values: no visible global function definition for ‘:=’
sponge_compute_p_values: no visible binding for global variable
  ‘cor_cut’
sponge_compute_p_values: no visible binding for global variable
  ‘df_cut’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘chunk’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘g_expr_batch’
sponge_gene_miRNA_interaction_filter : <anonymous>: no visible binding
  for global variable ‘g_expr_batch’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘gene’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘g_expr’
sponge_network: no visible binding for global variable ‘gene’
sponge_network: no visible binding for global variable ‘mir’
sponge_plot_network_centralities: no visible global function definition
  for ‘head’
sponge_plot_simulation_results: no visible binding for global variable
  ‘mscor’
sponge_run_benchmark: no visible binding for global variable
  ‘precomputed_cov_matrices’
sponge_run_benchmark: no visible binding for global variable
  ‘elastic.net’
sponge_run_benchmark: no visible binding for global variable
  ‘each.miRNA’
sponge_subsampling: no visible binding for global variable ‘sub.n’
sponge_subsampling: no visible binding for global variable ‘geneA’
sponge_subsampling: no visible binding for global variable ‘geneB’
Undefined global functions or variables:
  . .EACHI .I := J alpha attach.big.matrix chunk cor_cut cov.matrices.k
  cov.matrices.m cov.matrix df_cut dt.m each.miRNA elastic.net g_expr
  g_expr_batch gene geneA geneA_idx geneB geneB_idx gene_combis ginv
  head i k m mir mirna mscor mwhich p.adj p.val
  precomputed_cov_matrices solution sub.n
Consider adding
  importFrom("utils", "head")
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 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 or elapsed time > 5s
                                       user system elapsed
sponge_build_null_model              37.311 19.961  25.833
sponge_gene_miRNA_interaction_filter 40.781  1.343  41.512
sponge_run_benchmark                 11.385  0.101  11.588
sponge_compute_p_values               2.610  3.647   0.740
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/SPONGE.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 SPONGE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SPONGE’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SPONGE)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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(SPONGE)
> 
> test_check("SPONGE")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 167 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
141.703  32.310 134.899 

name	user	system	elapsed
check_and_convert_expression_data	0	0	0
sample_zero_mscor_cov	0.439	0.013	0.461
sample_zero_mscor_data	2.520	0.106	2.648
sponge	1.047	0.014	1.071
sponge_build_null_model	37.311	19.961	25.833
sponge_compute_p_values	2.610	3.647	0.740
sponge_edge_centralities	0.064	0.096	0.019
sponge_gene_miRNA_interaction_filter	40.781	1.343	41.512
sponge_network	0.017	0.005	0.022
sponge_node_centralities	0.011	0.002	0.013
sponge_plot_network	0.216	0.019	0.237
sponge_plot_network_centralities	0.000	0.000	0.001
sponge_plot_simulation_results	3.304	0.055	3.394
sponge_run_benchmark	11.385	0.101	11.588
sponge_subsampling	0.967	0.011	0.989