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CHECK report for mAPKL on tokay1

This page was generated on 2019-04-13 11:24:49 -0400 (Sat, 13 Apr 2019).

Package 874/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mAPKL 1.12.0
Argiris Sakellariou
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/mAPKL
Branch: RELEASE_3_8
Last Commit: dbedcd3
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: mAPKL
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mAPKL.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mAPKL_1.12.0.tar.gz
StartedAt: 2019-04-13 03:29:57 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:50:40 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 1242.5 seconds
RetCode: 0
Status:  OK  
CheckDir: mAPKL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mAPKL.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mAPKL_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/mAPKL.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mAPKL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mAPKL' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mAPKL          128.75   0.39  129.14
classification 119.44   0.92  123.79
netwAttr       117.47   0.20  117.68
preprocess      28.64   0.13   28.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
classification 120.39   0.57  120.99
mAPKL          108.08   0.43  108.52
netwAttr        99.12   0.40   99.55
preprocess      23.75   0.10   23.85
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/mAPKL_1.12.0.tar.gz && rm -rf mAPKL.buildbin-libdir && mkdir mAPKL.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mAPKL.buildbin-libdir mAPKL_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL mAPKL_1.12.0.zip && rm mAPKL_1.12.0.tar.gz mAPKL_1.12.0.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  988k  100  988k    0     0  13.2M      0 --:--:-- --:--:-- --:--:-- 13.9M

install for i386

* installing *source* package 'mAPKL' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mAPKL'
    finding HTML links ... done
    Annot-class                             html  
    Classify-class                          html  
    DataLD-class                            html  
    NetAttr-class                           html  
    annotate                                html  
    classification                          html  
    loadFiles                               html  
    mAPKL-package                           html  
    mAPKL                                   html  
    mAPKLRes-class                          html  
    metrics                                 html  
    netwAttr                                html  
    preprocess                              html  
    probes2pathways                         html  
    report                                  html  
    sampling                                html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mAPKL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mAPKL' as mAPKL_1.12.0.zip
* DONE (mAPKL)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'mAPKL' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

mAPKL.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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$trainData in C:/Users/biocbuild/bbs-3.8-bioc/meat/mAPKL.Rcheck/tests_i386
Saving density graph for breast$testData in C:/Users/biocbuild/bbs-3.8-bioc/meat/mAPKL.Rcheck/tests_i386
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 15 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


Attaching package: 'IRanges'

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

    windows

Loading required package: org.Hs.eg.db


'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 -- Sat Apr 13 03:48:32 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 
> 
> proc.time()
   user  system elapsed 
 134.57    1.39  136.07 

mAPKL.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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$trainData in C:/Users/biocbuild/bbs-3.8-bioc/meat/mAPKL.Rcheck/tests_x64
Saving density graph for breast$testData in C:/Users/biocbuild/bbs-3.8-bioc/meat/mAPKL.Rcheck/tests_x64
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 15 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


Attaching package: 'IRanges'

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

    windows

Loading required package: org.Hs.eg.db


'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 -- Sat Apr 13 03:50:34 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 
> 
> proc.time()
   user  system elapsed 
 120.46    0.87  121.35 

Example timings

mAPKL.Rcheck/examples_i386/mAPKL-Ex.timings

nameusersystemelapsed
annotate0.570.021.17
classification119.44 0.92123.79
mAPKL128.75 0.39129.14
metrics000
netwAttr117.47 0.20117.68
preprocess28.64 0.1328.77
probes2pathways0.310.060.37
report000
sampling1.330.031.36

mAPKL.Rcheck/examples_x64/mAPKL-Ex.timings

nameusersystemelapsed
annotate0.330.110.44
classification120.39 0.57120.99
mAPKL108.08 0.43108.52
metrics000
netwAttr99.12 0.4099.55
preprocess23.75 0.1023.85
probes2pathways0.380.060.43
report000
sampling1.200.001.21