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CHECK report for SPONGE on tokay2

This page was generated on 2019-04-09 12:32:18 -0400 (Tue, 09 Apr 2019).

Package 1546/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPONGE 1.5.0
Markus List
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SPONGE
Branch: master
Last Commit: 6d542ec
Last Changed Date: 2018-10-30 11:54:38 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: SPONGE
Version: 1.5.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SPONGE_1.5.0.tar.gz
StartedAt: 2019-04-09 06:09:18 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:17:00 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 461.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: SPONGE.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SPONGE_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SPONGE.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'SPONGE' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.3Mb
  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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
sponge_gene_miRNA_interaction_filter 25.66   0.11   25.76
sponge_build_null_model              18.50   0.05   18.55
sponge_run_benchmark                  9.51   0.03    9.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
sponge_gene_miRNA_interaction_filter 34.70   0.06   34.76
sponge_build_null_model              20.89   0.09   20.93
sponge_run_benchmark                 13.08   0.03   13.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  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
** running tests for arch 'x64' ...
  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: 2 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SPONGE.Rcheck/00check.log'
for details.

Installation output

SPONGE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SPONGE_1.5.0.tar.gz && rm -rf SPONGE.buildbin-libdir && mkdir SPONGE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SPONGE.buildbin-libdir SPONGE_1.5.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SPONGE_1.5.0.zip && rm SPONGE_1.5.0.tar.gz SPONGE_1.5.0.zip
###
##############################################################################
##############################################################################


  % 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 4103k  100 4103k    0     0  6362k      0 --:--:-- --:--:-- --:--:-- 6432k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'SPONGE' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SPONGE'
    finding HTML links ... done
    ceRNA_interactions                      html  
    check_and_convert_expression_data       html  
    fn_elasticnet                           html  
    fn_gene_miRNA_F_test                    html  
    fn_get_model_coef                       html  
    fn_get_rss                              html  
    fn_get_shared_miRNAs                    html  
    gene_expr                               html  
    genes_pairwise_combinations             html  
    mir_expr                                html  
    mir_interactions                        html  
    mircode_ensg                            html  
    mircode_symbol                          html  
    precomputed_cov_matrices                html  
    precomputed_null_model                  html  
    sample_zero_mscor_cov                   html  
    sample_zero_mscor_data                  html  
    sponge                                  html  
    sponge_build_null_model                 html  
    sponge_compute_p_values                 html  
    sponge_edge_centralities                html  
    sponge_gene_miRNA_interaction_filter    html  
    sponge_network                          html  
    sponge_node_centralities                html  
    sponge_plot_network                     html  
    sponge_plot_network_centralities        html  
    sponge_plot_simulation_results          html  
    sponge_run_benchmark                    html  
    sponge_subsampling                      html  
    targetscan_ensg                         html  
    targetscan_symbol                       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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'SPONGE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SPONGE' as SPONGE_1.5.0.zip
* DONE (SPONGE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SPONGE' successfully unpacked and MD5 sums checked

Tests output

SPONGE.Rcheck/tests_i386/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> 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: 0.081)
[1] -0.162902 - -0.014333 == -0.148570
[2] -0.141035 - -0.014073 == -0.126962
[3] -0.058932 -  0.000798 == -0.059730
[4]  0.000839 -  0.001341 == -0.000502
[5]  0.081292 -  0.012056 ==  0.069236

== 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

SPONGE.Rcheck/tests_x64/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> 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

Example timings

SPONGE.Rcheck/examples_i386/SPONGE-Ex.timings

nameusersystemelapsed
check_and_convert_expression_data000
sample_zero_mscor_cov0.240.020.25
sample_zero_mscor_data2.030.122.16
sponge0.690.020.70
sponge_build_null_model18.50 0.0518.55
sponge_compute_p_values1.020.330.86
sponge_edge_centralities0.010.000.02
sponge_gene_miRNA_interaction_filter25.66 0.1125.76
sponge_network0.010.000.02
sponge_node_centralities000
sponge_plot_network0.180.010.22
sponge_plot_network_centralities000
sponge_plot_simulation_results2.310.052.36
sponge_run_benchmark9.510.039.54
sponge_subsampling0.630.020.64

SPONGE.Rcheck/examples_x64/SPONGE-Ex.timings

nameusersystemelapsed
check_and_convert_expression_data000
sample_zero_mscor_cov0.360.000.36
sample_zero_mscor_data1.450.041.50
sponge0.710.020.72
sponge_build_null_model20.89 0.0920.93
sponge_compute_p_values0.690.080.69
sponge_edge_centralities0.000.000.01
sponge_gene_miRNA_interaction_filter34.70 0.0634.76
sponge_network0.020.000.02
sponge_node_centralities000
sponge_plot_network0.230.010.26
sponge_plot_network_centralities000
sponge_plot_simulation_results3.690.043.72
sponge_run_benchmark13.08 0.0313.11
sponge_subsampling1.030.001.03