Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SPONGE on tokay2

This page was generated on 2020-10-17 11:57:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SPONGE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1721/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPONGE 1.10.0
Markus List
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SPONGE
Branch: RELEASE_3_11
Last Commit: e4fa50d
Last Changed Date: 2020-04-27 15:09:48 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SPONGE
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SPONGE_1.10.0.tar.gz
StartedAt: 2020-10-17 08:33:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:41:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 473.4 seconds
RetCode: 0
Status:  OK  
CheckDir: SPONGE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPONGE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SPONGE_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SPONGE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.10.0'
* 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 'is'
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 global function definition for 'is'
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 global function
  definition for 'is'
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 is k m mir mirna mscor mwhich p.adj p.val
  precomputed_cov_matrices solution sub.n
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 (user + system) or elapsed time > 5s
                                      user system elapsed
sponge_gene_miRNA_interaction_filter 38.86   0.22   39.10
sponge_build_null_model              23.81   0.02   23.83
sponge_run_benchmark                 13.80   0.01   13.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
sponge_gene_miRNA_interaction_filter 29.97   0.08   30.05
sponge_build_null_model              18.00   0.01   18.02
sponge_run_benchmark                 14.04   0.01   14.06
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/SPONGE.Rcheck/00check.log'
for details.



Installation output

SPONGE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SPONGE_1.10.0.tar.gz && rm -rf SPONGE.buildbin-libdir && mkdir SPONGE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SPONGE.buildbin-libdir SPONGE_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SPONGE_1.10.0.zip && rm SPONGE_1.10.0.tar.gz SPONGE_1.10.0.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 4104k  100 4104k    0     0  38.5M      0 --:--:-- --:--:-- --:--:-- 41.3M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'SPONGE' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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_1.10.0.zip
* DONE (SPONGE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SPONGE' successfully unpacked and MD5 sums checked

Tests output

SPONGE.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(SPONGE)
> 
> test_check("SPONGE")
== testthat results  ===========================================================
[ OK: 163 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  81.79    0.89   97.82 

SPONGE.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(SPONGE)
> 
> test_check("SPONGE")
== testthat results  ===========================================================
[ OK: 163 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  84.00    0.43   99.59 

Example timings

SPONGE.Rcheck/examples_i386/SPONGE-Ex.timings

nameusersystemelapsed
check_and_convert_expression_data000
sample_zero_mscor_cov0.310.010.33
sample_zero_mscor_data1.790.081.88
sponge0.690.010.70
sponge_build_null_model23.81 0.0223.83
sponge_compute_p_values0.550.000.55
sponge_edge_centralities0.010.000.01
sponge_gene_miRNA_interaction_filter38.86 0.2239.10
sponge_network0.020.000.01
sponge_node_centralities000
sponge_plot_network0.170.030.20
sponge_plot_network_centralities000
sponge_plot_simulation_results3.640.033.68
sponge_run_benchmark13.80 0.0113.81
sponge_subsampling0.620.000.62

SPONGE.Rcheck/examples_x64/SPONGE-Ex.timings

nameusersystemelapsed
check_and_convert_expression_data000
sample_zero_mscor_cov0.360.000.36
sample_zero_mscor_data2.250.032.28
sponge0.930.000.97
sponge_build_null_model18.00 0.0118.02
sponge_compute_p_values0.360.000.36
sponge_edge_centralities0.020.000.01
sponge_gene_miRNA_interaction_filter29.97 0.0830.05
sponge_network0.010.000.01
sponge_node_centralities000
sponge_plot_network0.240.020.27
sponge_plot_network_centralities000
sponge_plot_simulation_results3.080.003.08
sponge_run_benchmark14.04 0.0114.06
sponge_subsampling1.080.021.09