Oleg Mayba
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MBASED |
| Branch: RELEASE_3_9 |
| Last Commit: 4a22826 |
| Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:53:48 -0400 (Wed, 16 Oct 2019).
| Package 930/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MBASED 1.18.0 Oleg Mayba
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MBASED |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MBASED.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MBASED_1.18.0.tar.gz |
| StartedAt: 2019-10-16 04:18:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:23:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 291.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MBASED.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MBASED.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MBASED_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MBASED.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBASED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MBASED’ version ‘1.18.0’
* 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 ‘MBASED’ 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 ... NOTE
MBASEDMetaAnalysis: no visible global function definition for ‘pchisq’
MBASEDMetaAnalysis: no visible global function definition for ‘pnorm’
maxLogLikelihoodCalculator1s: no visible global function definition for
‘optimize’
maxLogLikelihoodCalculator2s: no visible global function definition for
‘optimize’
runMBASED: no visible global function definition for ‘is’
runMBASED1s: no visible global function definition for ‘is’
runMBASED2s: no visible global function definition for ‘is’
vectorizedRbetabinomAB: no visible global function definition for
‘rbeta’
vectorizedRbetabinomAB: no visible global function definition for
‘rbinom’
vectorizedRbetabinomMR: no visible global function definition for
‘rbeta’
vectorizedRbetabinomMR: no visible global function definition for
‘rbinom’
Undefined global functions or variables:
is optimize pchisq pnorm rbeta rbinom
Consider adding
importFrom("methods", "is")
importFrom("stats", "optimize", "pchisq", "pnorm", "rbeta", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/MBASED.Rcheck/00check.log’
for details.
MBASED.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MBASED ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MBASED’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (MBASED)
MBASED.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-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("MBASED")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
RUNIT TEST PROTOCOL -- Wed Oct 16 04:23:35 2019
***********************************************
Number of test functions: 21
Number of errors: 0
Number of failures: 0
1 Test Suite :
MBASED RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
80.586 2.232 83.211
MBASED.Rcheck/MBASED-Ex.timings
| name | user | system | elapsed | |
| FreemanTukeyFunctions | 1.660 | 0.074 | 1.790 | |
| MBASEDMetaAnalysis | 0.007 | 0.001 | 0.008 | |
| MBASEDMetaAnalysisGetMeansAndSEs | 0.002 | 0.001 | 0.002 | |
| MBASEDVectorizedMetaprop | 0.010 | 0.002 | 0.011 | |
| MBASEDVectorizedPropDiffTest | 0.005 | 0.001 | 0.007 | |
| betaParametrizationConverters | 0.001 | 0.001 | 0.003 | |
| estimateMAF1s | 0.013 | 0.001 | 0.013 | |
| estimateMAF2s | 0.008 | 0.001 | 0.008 | |
| generatingBetaBinomialCounts | 0.002 | 0.001 | 0.002 | |
| getPFinal | 0.002 | 0.001 | 0.002 | |
| getSimulationPvalue | 0.001 | 0.001 | 0.001 | |
| logLikelihoodCalculator1s | 0.000 | 0.001 | 0.002 | |
| logLikelihoodCalculator2s | 0.001 | 0.001 | 0.002 | |
| maxLogLikelihoodCalculator1s | 0.001 | 0.000 | 0.001 | |
| maxLogLikelihoodCalculator2s | 0.001 | 0.000 | 0.002 | |
| runMBASED | 0.000 | 0.000 | 0.001 | |
| runMBASED1s | 0.000 | 0.000 | 0.001 | |
| runMBASED1s1aseID | 0.000 | 0.000 | 0.001 | |
| runMBASED2s | 0.001 | 0.001 | 0.001 | |
| runMBASED2s1aseID | 0.001 | 0.000 | 0.000 | |
| shiftAndAttenuateProportions | 0.002 | 0.001 | 0.003 | |