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CHECK report for mAPKL on malbec2

This page was generated on 2019-10-16 12:06:02 -0400 (Wed, 16 Oct 2019).

Package 913/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mAPKL 1.14.1
Argiris Sakellariou
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/mAPKL
Branch: RELEASE_3_9
Last Commit: 04bcb3a
Last Changed Date: 2019-05-24 12:17:26 -0400 (Fri, 24 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: mAPKL
Version: 1.14.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings mAPKL_1.14.1.tar.gz
StartedAt: 2019-10-16 02:51:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:04:03 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 726.6 seconds
RetCode: 0
Status:  OK 
CheckDir: mAPKL.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings mAPKL_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/mAPKL.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mAPKL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mAPKL’ version ‘1.14.1’
* 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 ‘mAPKL’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mAPKL          139.524  0.124 139.700
classification 139.311  0.207 139.722
netwAttr       131.514  0.060 131.294
preprocess      28.628  0.052  28.680
* 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

mAPKL.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL mAPKL
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘mAPKL’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
   ‘mAPKL.Rnw’ 
** 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 (mAPKL)

Tests output

mAPKL.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> BiocGenerics:::testPackage("mAPKL")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Assign 60% as train data and 40% as test data
Saving density graph for breast$trainData in /home/biocbuild/bbs-3.9-bioc/meat/mAPKL.Rcheck/tests
Saving density graph for breast$testData in /home/biocbuild/bbs-3.9-bioc/meat/mAPKL.Rcheck/tests
b=10	b=20	b=30	b=40	b=50	b=60	b=70	b=80	b=90	b=100	
b=110	b=120	b=130	b=140	b=150	b=160	b=170	b=180	b=190	b=200	
b=210	b=220	b=230	b=240	b=250	b=260	b=270	b=280	b=290	b=300	
b=310	b=320	b=330	b=340	b=350	b=360	b=370	b=380	b=390	b=400	
b=410	b=420	b=430	b=440	b=450	b=460	b=470	b=480	b=490	b=500	
b=510	b=520	b=530	b=540	b=550	b=560	b=570	b=580	b=590	b=600	
b=610	b=620	b=630	b=640	b=650	b=660	b=670	b=680	b=690	b=700	
b=710	b=720	b=730	b=740	b=750	b=760	b=770	b=780	b=790	b=800	
b=810	b=820	b=830	b=840	b=850	b=860	b=870	b=880	b=890	b=900	
b=910	b=920	b=930	b=940	b=950	b=960	b=970	b=980	b=990	b=1000	
Please wait! The (KL) cluster indexing may take several minutes...
Asking for 22 number of clusters
fc according to limma
Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: org.Hs.eg.db


'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Negative samples: 8
Positive samples: 4
TN=6
FP=2
TP=3
FN=1
AUC=0.75
Accuracy=75.00
MCC=0.48
Specificity=0.75
Sensitivity=0.75
Assign 60% as train data and 40% as test data


RUNIT TEST PROTOCOL -- Wed Oct 16 03:03:59 2019 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mAPKL RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .local(s, x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
2: In .local(s, x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
3: In .local(s, x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
4: In .local(s, x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
> 
> proc.time()
   user  system elapsed 
155.083   0.775 155.966 

Example timings

mAPKL.Rcheck/mAPKL-Ex.timings

nameusersystemelapsed
annotate0.7790.0240.864
classification139.311 0.207139.722
mAPKL139.524 0.124139.700
metrics0.0020.0000.002
netwAttr131.514 0.060131.294
preprocess28.628 0.05228.680
probes2pathways0.8380.0361.042
report0.0000.0000.001
sampling1.2340.0161.251