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CHECK report for Mirsynergy on merida1

This page was generated on 2019-04-16 11:57:26 -0400 (Tue, 16 Apr 2019).

Package 976/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mirsynergy 1.18.0
Yue Li
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Mirsynergy
Branch: RELEASE_3_8
Last Commit: 2410e04
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Mirsynergy
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mirsynergy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mirsynergy_1.18.0.tar.gz
StartedAt: 2019-04-16 01:20:34 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:21:45 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 71.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Mirsynergy.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mirsynergy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mirsynergy_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Mirsynergy.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 ‘Mirsynergy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mirsynergy’ version ‘1.18.0’
* 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 ‘Mirsynergy’ 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
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

Installation output

Mirsynergy.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Mirsynergy
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Mirsynergy’ ...
** R
** inst
** 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 (Mirsynergy)

Tests output

Mirsynergy.Rcheck/tests/runTests.Rout


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.

> BiocGenerics:::testPackage("Mirsynergy")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Discard row/column of all zeros in W

*Stage I. Cluster 18 miRNA:


Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141

Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100

Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168

Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086

Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097

Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120

Forming new module with seed: miRNA5

MRM before merging:
M1 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M2 (synergy=0.14089190465843): 
miRNA3 miRNA9 
M3 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M4 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M5 (synergy=0.0995481886856942): 
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17 
M6 (synergy=0.167919254849307): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
M7 (synergy=0.0857963527273969): 
miRNA1 miRNA19 
M8 (synergy=0.0970569736542555): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
M9 (synergy=0.119598648023761): 
miRNA3 miRNA9 miRNA11 
M10 (synergy=0): 
miRNA5 
Merge cluster threshold: overlap >= 0.80:


MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01): 
miRNA6 miRNA8 miRNA12 miRNA18 
M2 (density=7.35e-01; synergy=1.41e-01): 
miRNA3 miRNA9 
M3 (density=9.31e-02; synergy=9.71e-02): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
M4 (density=1.19e-01; synergy=1.68e-01): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
M5 (density=3.75e-01; synergy=8.58e-02): 
miRNA1 miRNA19 
M6 (density=2.88e-01; synergy=1.2e-01): 
miRNA3 miRNA9 miRNA11 

Time elapsed for Stage I: 0.060

*Stage II. Grow MRM with mRNA:


Forming new module with seed: miRNA3,miRNA9

Forming new module with seed: miRNA6,miRNA8,miRNA12,miRNA18
add: mRNA12; w.in: 1.013; w.bound: 1.330; new synergy: 0.121
add: mRNA1; w.in: 1.926; w.bound: 1.715; new synergy: 0.165
add: mRNA9; w.in: 1.225; w.bound: 1.604; new synergy: 0.095
add: mRNA16; w.in: 2.219; w.bound: 2.509; new synergy: 0.133

Forming new module with seed: miRNA2,miRNA6,miRNA8,miRNA12,miRNA16,miRNA17,miRNA18,miRNA20
add: mRNA2; w.in: 3.191; w.bound: 2.584; new synergy: 0.161
add: mRNA9; w.in: 1.429; w.bound: 4.699; new synergy: 0.059
add: mRNA20; w.in: 3.895; w.bound: 3.289; new synergy: 0.168
add: mRNA16; w.in: 2.423; w.bound: 5.604; new synergy: 0.086

Forming new module with seed: miRNA2,miRNA7,miRNA10,miRNA14,miRNA15,miRNA17
add: mRNA2; w.in: 4.299; w.bound: 3.872; new synergy: 0.142
add: mRNA2; w.in: 1.047; w.bound: 4.678; new synergy: 0.053
add: mRNA14; w.in: 4.984; w.bound: 3.470; new synergy: 0.154
add: mRNA16; w.in: 2.020; w.bound: 5.626; new synergy: 0.085
add: mRNA1; w.in: 5.747; w.bound: 4.154; new synergy: 0.160
add: mRNA10; w.in: 2.900; w.bound: 5.695; new synergy: 0.109
add: mRNA20; w.in: 6.985; w.bound: 3.791; new synergy: 0.180
add: mRNA17; w.in: 3.766; w.bound: 5.134; new synergy: 0.130
add: mRNA12; w.in: 7.650; w.bound: 4.341; new synergy: 0.182
add: mRNA13; w.in: 4.519; w.bound: 4.381; new synergy: 0.146

Forming new module with seed: miRNA3,miRNA9,miRNA11
add: mRNA6; w.in: 5.207; w.bound: 3.693; new synergy: 0.158
add: mRNA12; w.in: 1.013; w.bound: 2.104; new synergy: 0.091
add: mRNA1; w.in: 1.926; w.bound: 2.488; new synergy: 0.134
add: mRNA19; w.in: 2.584; w.bound: 2.331; new synergy: 0.153
add: mRNA20; w.in: 5.911; w.bound: 4.398; new synergy: 0.163
add: mRNA8; w.in: 3.060; w.bound: 2.037; new synergy: 0.160
add: mRNA1; w.in: 7.038; w.bound: 4.354; new synergy: 0.179
add: mRNA12; w.in: 7.905; w.bound: 4.499; new synergy: 0.186
add: mRNA15; w.in: 8.304; w.bound: 4.101; new synergy: 0.187

Forming new module with seed: miRNA1,miRNA19
add: mRNA20; w.in: 0.861; w.bound: 1.365; new synergy: 0.105
add: mRNA16; w.in: 1.565; w.bound: 2.850; new synergy: 0.126
add: mRNA2; w.in: 2.537; w.bound: 2.925; new synergy: 0.164

Final MRM:
M1 (density=4.43e-02; synergy=1.68e-01): 
miRNA6 miRNA8 miRNA12 miRNA18 
mRNA2 mRNA9 mRNA16 mRNA20 
M2 (density=9.63e-02; synergy=1.65e-01): 
miRNA3 miRNA9 
mRNA1 mRNA12 
M3 (density=2.47e-02; synergy=1.87e-01): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
mRNA1 mRNA2 mRNA6 mRNA10 mRNA12 mRNA13 mRNA15 mRNA16 mRNA17 mRNA20 
M4 (density=2.32e-02; synergy=1.82e-01): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
mRNA1 mRNA2 mRNA9 mRNA12 mRNA14 mRNA16 mRNA20 
M5 (density=8.46e-02; synergy=1.64e-01): 
miRNA1 miRNA19 
mRNA2 mRNA16 mRNA20 
M6 (density=4.86e-02; synergy=1.6e-01): 
miRNA3 miRNA9 miRNA11 
mRNA1 mRNA8 mRNA12 mRNA19 

Total time elapsed: 0.349 (sec)


RUNIT TEST PROTOCOL -- Tue Apr 16 01:21:40 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Mirsynergy RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.181   0.382   3.407

Example timings

Mirsynergy.Rcheck/Mirsynergy-Ex.timings

nameusersystemelapsed
mirsynergy0.4280.3270.436
plot_module_summary1.0720.0991.179
plot_modules0.1790.0040.185
print_modules20.0030.0010.003
summary_modules0.0080.0010.009
tabular_module0.0380.0060.044
tcga_brca_testdata0.4450.0320.481
toy_modules0.0010.0000.001