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CHECK report for mAPKL on tokay1

This page was generated on 2021-05-06 12:32:06 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the mAPKL package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 997/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mAPKL 1.20.0  (landing page)
Argiris Sakellariou
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/mAPKL
Branch: RELEASE_3_12
Last Commit: 68b77e0
Last Changed Date: 2020-10-27 11:01:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: mAPKL
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mAPKL.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings mAPKL_1.20.0.tar.gz
StartedAt: 2021-05-06 04:14:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:37:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 1352.5 seconds
RetCode: 0
Status:   OK   
CheckDir: mAPKL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mAPKL.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings mAPKL_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/mAPKL.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.20.0'
* 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 '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 (user + system) or elapsed time > 5s
                 user system elapsed
netwAttr       162.27   0.46  163.90
classification 137.92   1.06  140.22
mAPKL          121.65   0.57  122.25
preprocess      37.23   0.19   37.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
netwAttr       120.45   0.37  120.85
classification 112.72   0.45  113.17
mAPKL          110.88   0.27  111.14
preprocess      28.56   0.21   28.76
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/mAPKL_1.20.0.tar.gz && rm -rf mAPKL.buildbin-libdir && mkdir mAPKL.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mAPKL.buildbin-libdir mAPKL_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL mAPKL_1.20.0.zip && rm mAPKL_1.20.0.tar.gz mAPKL_1.20.0.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 4865k  100 4865k    0     0  70.3M      0 --:--:-- --:--:-- --:--:-- 70.9M

install for i386

* installing *source* package 'mAPKL' ...
** using staged installation
** 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 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

* installing *source* package 'mAPKL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mAPKL' as mAPKL_1.20.0.zip
* DONE (mAPKL)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'mAPKL' successfully unpacked and MD5 sums checked

Tests output

mAPKL.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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, 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.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$trainData in C:/Users/biocbuild/bbs-3.12-bioc/meat/mAPKL.Rcheck/tests_i386
Saving density graph for breast$testData in C:/Users/biocbuild/bbs-3.12-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 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


Attaching package: 'IRanges'

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

    windows

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 -- Thu May 06 04:34:26 2021 
*********************************************** 
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 = 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 = 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 = 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 = 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 
 161.09    2.17  163.26 

mAPKL.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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, 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.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$trainData in C:/Users/biocbuild/bbs-3.12-bioc/meat/mAPKL.Rcheck/tests_x64
Saving density graph for breast$testData in C:/Users/biocbuild/bbs-3.12-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 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


Attaching package: 'IRanges'

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

    windows

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 -- Thu May 06 04:37:16 2021 
*********************************************** 
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 = 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 = 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 = 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 = 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 
 168.23    1.62  169.84 

Example timings

mAPKL.Rcheck/examples_i386/mAPKL-Ex.timings

nameusersystemelapsed
annotate0.590.330.94
classification137.92 1.06140.22
mAPKL121.65 0.57122.25
metrics000
netwAttr162.27 0.46163.90
preprocess37.23 0.1937.44
probes2pathways1.020.051.06
report000
sampling1.630.061.68

mAPKL.Rcheck/examples_x64/mAPKL-Ex.timings

nameusersystemelapsed
annotate0.620.110.73
classification112.72 0.45113.17
mAPKL110.88 0.27111.14
metrics000
netwAttr120.45 0.37120.85
preprocess28.56 0.2128.76
probes2pathways1.050.041.10
report000
sampling1.550.081.62