Package: SPONGE

Version: 1.5.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SPONGE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SPONGE_1.5.0.tar.gz

StartedAt: 2019-04-09 03:50:47 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:55:14 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 267.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: SPONGE.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SPONGE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SPONGE_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SPONGE.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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_gene_miRNA_interaction_filter 31.371  0.092  31.489
sponge_compute_p_values              26.897  0.103   3.658
sponge_build_null_model              22.343  0.004  20.463
sponge_run_benchmark                 13.882  0.000  13.883
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 142 SKIPPED: 0 FAILED: 25
  1. Failure: TEST computing residual sum of squares (@test_elastic_net.R#9) 
  2. Failure: TEST extract model coefficients (@test_elastic_net.R#17) 
  3. Failure: TEST extract model coefficients (@test_elastic_net.R#19) 
  4. Failure: TEST elastic net (@test_elastic_net.R#27) 
  5. Failure: TEST elastic net (@test_elastic_net.R#28) 
  6. Failure: TEST elastic net (@test_elastic_net.R#29) 
  7. Failure: TEST F test (@test_elastic_net.R#37) 
  8. Failure: TEST F test (@test_elastic_net.R#39) 
  9. Failure: Regression filter works with one interaction db (@test_regression_filter.R#19) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SPONGE.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SPONGE
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SPONGE’ ...
** using staged installation
** 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 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 (SPONGE)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
── 1. Failure: TEST computing residual sum of squares (@test_elastic_net.R#9)  ─
fn_get_rss(model, mir_expr, gene_expr[, 2]) not equal to 7.730392.
1/1 mismatches
[1] 7.49 - 7.73 == -0.237

── 2. Failure: TEST extract model coefficients (@test_elastic_net.R#17)  ───────
nrow(fn_get_model_coef(model)) not equal to 44.
1/1 mismatches
[1] 49 - 44 == 5

── 3. Failure: TEST extract model coefficients (@test_elastic_net.R#19)  ───────
mean(fn_get_model_coef(model)$coefficient) not equal to -0.01546664.
1/1 mismatches
[1] -0.0165 - -0.0155 == -0.00107

── 4. Failure: TEST elastic net (@test_elastic_net.R#27)  ──────────────────────
result$lambda.min not equal to 0.2805692.
1/1 mismatches
[1] 0.0307 - 0.281 == -0.25

── 5. Failure: TEST elastic net (@test_elastic_net.R#28)  ──────────────────────
result$lambda[1] not equal to 576.9941.
1/1 mismatches
[1] 1.15 - 577 == -576

── 6. Failure: TEST elastic net (@test_elastic_net.R#29)  ──────────────────────
result$lambda has length 71, not length 99.

── 7. Failure: TEST F test (@test_elastic_net.R#37)  ───────────────────────────
nrow(result) not equal to 50.
1/1 mismatches
[1] 44 - 50 == -6

── 8. Failure: TEST F test (@test_elastic_net.R#39)  ───────────────────────────
mean(result$p.adj) not equal to 0.02068886.
1/1 mismatches
[1] 0.153 - 0.0207 == 0.132

── 9. Failure: Regression filter works with one interaction db (@test_regression
genes_miRNA_candidates$ASAP2$coefficient not equal to -0.2553748.
1/1 mismatches
[1] -0.246 - -0.255 == 0.0094

── 10. Failure: Regression filter accepts ExpressionSet as input (@test_regressi
genes_miRNA_candidates$ASAP2$coefficient not equal to -0.2553748.
1/1 mismatches
[1] -0.246 - -0.255 == 0.0094

── 11. Failure: Regression filter works with stricter threshold (@test_regressio
genes_miRNA_candidates$ASAP2$coefficient not equal to -0.2553748.
1/1 mismatches
[1] -0.246 - -0.255 == 0.0094

── 12. Failure: Regression filter works without mir interaction db (@test_regres
nrow(genes_miRNA_candidates$ASAP2) not equal to 18.
1/1 mismatches
[1] 19 - 18 == 1

── 13. Failure: Regression filter works with several mir interaction dbs (@test_
nrow(genes_miRNA_candidates$ASAP2) not equal to 16.
1/1 mismatches
[1] 15 - 16 == -1

── 14. Failure: Regression filter works with several mir interaction dbs (@test_
nrow(genes_miRNA_candidates$DNMT3A) not equal to 8.
1/1 mismatches
[1] 9 - 8 == 1

── 15. Failure: Regression filter works without threshold (@test_regression_filt
nrow(genes_miRNA_candidates$ASAP2) not equal to 25.
1/1 mismatches
[1] 23 - 25 == -2

── 16. Failure: Regression filter works without threshold (@test_regression_filt
nrow(genes_miRNA_candidates$DNMT3A) not equal to 18.
1/1 mismatches
[1] 19 - 18 == 1

── 17. Failure: Regression filter works with F-test (@test_regression_filter.R#1
nrow(genes_miRNA_candidates$ASAP2) not equal to 36.
1/1 mismatches
[1] 31 - 36 == -5

── 18. Failure: Regression filter works with F-test (@test_regression_filter.R#1
nrow(genes_miRNA_candidates$DNMT3A) not equal to 24.
1/1 mismatches
[1] 25 - 24 == 1

── 19. Failure: Regression filter works with F-test and p.adj cutoff (@test_regr
nrow(genes_miRNA_candidates$ASAP2) not equal to 13.
1/1 mismatches
[1] 16 - 13 == 3

── 20. Failure: Regression filter works in no targets mode (@test_regression_fil
nrow(genes_miRNA_candidates$ASAP2) not equal to 3.
1/1 mismatches
[1] 4 - 3 == 1

── 21. Failure: Regression filter with variance threshold (@test_regression_filt
nrow(genes_miRNA_candidates$ASAP2) not equal to 12.
1/1 mismatches
[1] 14 - 12 == 2

── 22. Failure: Regression filter with variance threshold (@test_regression_filt
nrow(genes_miRNA_candidates$DNMT3A) not equal to 6.
1/1 mismatches
[1] 7 - 6 == 1

── 23. Failure: Regression filter works with parallelization (@test_regression_f
nrow(genes_miRNA_candidates$ASAP2) not equal to 16.
1/1 mismatches
[1] 15 - 16 == -1

── 24. Failure: Regression filter works with parallelization (@test_regression_f
nrow(genes_miRNA_candidates$DNMT3A) not equal to 8.
1/1 mismatches
[1] 9 - 8 == 1

── 25. Failure: drawing sample data from a set of covariance matrices works (@te
...$NULL not equal to c(-0.0143328443, -0.0140734899, 0.0007982788, 0.001340915, 0.012055526).
5/5 mismatches (average diff: 0.0786)
[1] -0.162902 - -0.014333 == -1.49e-01
[2] -0.141035 - -0.014073 == -1.27e-01
[3]  0.000839 -  0.000798 ==  4.11e-05
[4]  0.049706 -  0.001341 ==  4.84e-02
[5]  0.081292 -  0.012056 ==  6.92e-02

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 142 SKIPPED: 0 FAILED: 25
1. Failure: TEST computing residual sum of squares (@test_elastic_net.R#9) 
2. Failure: TEST extract model coefficients (@test_elastic_net.R#17) 
3. Failure: TEST extract model coefficients (@test_elastic_net.R#19) 
4. Failure: TEST elastic net (@test_elastic_net.R#27) 
5. Failure: TEST elastic net (@test_elastic_net.R#28) 
6. Failure: TEST elastic net (@test_elastic_net.R#29) 
7. Failure: TEST F test (@test_elastic_net.R#37) 
8. Failure: TEST F test (@test_elastic_net.R#39) 
9. Failure: Regression filter works with one interaction db (@test_regression_filter.R#19) 
1. ...

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
check_and_convert_expression_data	0	0	0
sample_zero_mscor_cov	0.380	0.004	0.384
sample_zero_mscor_data	2.258	0.032	2.291
sponge	0.741	0.004	0.745
sponge_build_null_model	22.343	0.004	20.463
sponge_compute_p_values	26.897	0.103	3.658
sponge_edge_centralities	0.020	0.000	0.117
sponge_gene_miRNA_interaction_filter	31.371	0.092	31.489
sponge_network	0.01	0.00	0.01
sponge_node_centralities	0.006	0.000	0.006
sponge_plot_network	0.114	0.004	0.117
sponge_plot_network_centralities	0	0	0
sponge_plot_simulation_results	2.052	0.008	2.060
sponge_run_benchmark	13.882	0.000	13.883
sponge_subsampling	0.914	0.012	0.926