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This page was generated on 2022-01-21 13:08:00 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for mAPKL on machv2


To the developers/maintainers of the mAPKL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mAPKL.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1043/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mAPKL 1.24.0  (landing page)
Argiris Sakellariou
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/mAPKL
git_branch: RELEASE_3_14
git_last_commit: b9e43cb
git_last_commit_date: 2021-10-26 12:18:26 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mAPKL
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mAPKL_1.24.0.tar.gz
StartedAt: 2022-01-20 14:36:58 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:52:36 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 937.8 seconds
RetCode: 0
Status:   OK  
CheckDir: mAPKL.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mAPKL_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/mAPKL.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.24.0’
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
classification 176.655  2.726 179.634
mAPKL          168.787  2.428 171.498
netwAttr       166.209  2.280 168.658
preprocess      34.869  0.700  35.601
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mAPKL
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
** 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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("mAPKL")

Attaching package: 'BiocGenerics'

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$trainData in /Users/biocbuild/bbs-3.14-bioc/meat/mAPKL.Rcheck/tests
Saving density graph for breast$testData in /Users/biocbuild/bbs-3.14-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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: org.Hs.eg.db


'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 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 Jan 20 14:52:28 2022 
*********************************************** 
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 xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
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'.
5: 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'.
6: 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'.
7: 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'.
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
9: In xtfrm.data.frame(x) : cannot xtfrm data frames
10: In xtfrm.data.frame(x) : cannot xtfrm data frames
> 
> proc.time()
   user  system elapsed 
181.242   3.311 184.721 

Example timings

mAPKL.Rcheck/mAPKL-Ex.timings

nameusersystemelapsed
annotate1.2450.0371.284
classification176.655 2.726179.634
mAPKL168.787 2.428171.498
metrics0.0040.0000.004
netwAttr166.209 2.280168.658
preprocess34.869 0.70035.601
probes2pathways0.9810.0461.029
report0.0000.0000.001
sampling1.4230.0161.440