Argiris Sakellariou
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/mAPKL |
| Branch: RELEASE_3_10 |
| Last Commit: d6cd4e0 |
| Last Changed Date: 2019-10-29 13:09:08 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:41:19 -0400 (Wed, 15 Apr 2020).
| Package 950/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mAPKL 1.16.0 Argiris Sakellariou
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | ERROR | OK | ERROR | ERROR | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: mAPKL |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mAPKL_1.16.0.tar.gz |
| StartedAt: 2020-04-15 03:33:09 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:46:37 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 808.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mAPKL.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mAPKL_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/mAPKL.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/mAPKL.Rcheck/00install.out’ for details.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
classification 157.744 4.538 163.569
netwAttr 150.741 5.476 156.160
mAPKL 140.047 4.949 146.642
preprocess 33.432 2.002 35.777
* 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: 1 WARNING
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/mAPKL.Rcheck/00check.log’
for details.
mAPKL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mAPKL ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘mAPKL’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ‘mAPKL.Rnw’ ** testing if installed package can be loaded from temporary location Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. ** testing if installed package can be loaded from final location Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. ** testing if installed package keeps a record of temporary installation path * DONE (mAPKL)
mAPKL.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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("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$trainData in /Users/biocbuild/bbs-3.10-bioc/meat/mAPKL.Rcheck/tests
Saving density graph for breast$testData in /Users/biocbuild/bbs-3.10-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 Apr 15 03:46:31 2020
***********************************************
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 rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
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'.
5: 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'.
6: 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
164.015 5.163 170.773
mAPKL.Rcheck/mAPKL-Ex.timings
| name | user | system | elapsed | |
| annotate | 0.998 | 0.055 | 1.060 | |
| classification | 157.744 | 4.538 | 163.569 | |
| mAPKL | 140.047 | 4.949 | 146.642 | |
| metrics | 0.003 | 0.000 | 0.003 | |
| netwAttr | 150.741 | 5.476 | 156.160 | |
| preprocess | 33.432 | 2.002 | 35.777 | |
| probes2pathways | 0.911 | 0.037 | 0.955 | |
| report | 0 | 0 | 0 | |
| sampling | 1.351 | 0.068 | 1.432 | |