Caitlin McHugh
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cpvSNP |
| Branch: RELEASE_3_8 |
| Last Commit: 483b769 |
| Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:12 -0400 (Tue, 16 Apr 2019).
| Package 341/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cpvSNP 1.14.0 Caitlin McHugh
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: cpvSNP |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cpvSNP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cpvSNP_1.14.0.tar.gz |
| StartedAt: 2019-04-15 23:16:38 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:21:22 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 283.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cpvSNP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cpvSNP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cpvSNP_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/cpvSNP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cpvSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cpvSNP’ version ‘1.14.0’
* 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 ‘cpvSNP’ 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 ... NOTE
'library' or 'require' call to ‘GSEABase’ which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assocPvalBySetPlot: no visible global function definition for ‘rgb’
assocPvalBySetPlot: no visible global function definition for ‘col2rgb’
assocPvalBySetPlot : <anonymous>: no visible global function definition
for ‘density’
assocPvalBySetPlot: no visible global function definition for ‘plot’
assocPvalBySetPlot: no visible global function definition for ‘legend’
assocPvalBySetPlot: no visible global function definition for ‘polygon’
assocPvalBySetPlot: no visible global function definition for ‘lines’
assocPvalBySetPlot: no visible global function definition for ‘points’
createArrayData: no visible global function definition for ‘GRanges’
createArrayData: no visible global function definition for ‘Rle’
createArrayData: no visible global function definition for ‘IRanges’
createArrayData: no visible global function definition for
‘elementMetadata<-’
geneToSNPList: no visible global function definition for ‘findOverlaps’
glossiMarginal: no visible global function definition for ‘pgamma’
plotPvals: no visible binding for global variable ‘df’
plotPvals: no visible binding for global variable ‘pval’
simulate_chisq: no visible global function definition for ‘rnorm’
vegasMarginal: no visible global function definition for ‘rbinom’
vegasMarginal: no visible global function definition for ‘qchisq’
vegasPrep: no visible global function definition for ‘elementMetadata’
show,VEGASResult: no visible global function definition for ‘var’
Undefined global functions or variables:
GRanges IRanges Rle col2rgb density df elementMetadata
elementMetadata<- findOverlaps legend lines pgamma plot points
polygon pval qchisq rbinom rgb rnorm var
Consider adding
importFrom("grDevices", "col2rgb", "rgb")
importFrom("graphics", "legend", "lines", "plot", "points", "polygon")
importFrom("stats", "density", "df", "pgamma", "qchisq", "rbinom",
"rnorm", "var")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/cpvSNP.Rcheck/00check.log’
for details.
cpvSNP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cpvSNP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘cpvSNP’ ... ** R ** data ** 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 * DONE (cpvSNP)
cpvSNP.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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("cpvSNP")
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
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: 'graph'
The following object is masked from 'package:XML':
addNode
making GRanges object
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
RUNIT TEST PROTOCOL -- Mon Apr 15 23:21:12 2019
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
cpvSNP RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
Warning message:
In mode(current) : NAs introduced by coercion
>
> proc.time()
user system elapsed
19.266 1.818 20.876
cpvSNP.Rcheck/cpvSNP-Ex.timings
| name | user | system | elapsed | |
| GLOSSIResult-class | 0.002 | 0.000 | 0.002 | |
| GLOSSIResultCollection-class | 0.000 | 0.000 | 0.001 | |
| GeneSetResult-class | 0.001 | 0.001 | 0.001 | |
| GeneSetResultCollection-class | 0.001 | 0.000 | 0.002 | |
| VEGASResult-class | 0.001 | 0.000 | 0.001 | |
| VEGASResultCollection-class | 0.001 | 0.001 | 0.001 | |
| createArrayData | 0.263 | 0.024 | 0.292 | |
| degreesOfFreedom-method | 0.001 | 0.001 | 0.000 | |
| geneSetAnalysis | 0.181 | 0.013 | 0.196 | |
| geneSetName-methods | 0 | 0 | 0 | |
| geneToSNPList | 3.417 | 0.731 | 3.670 | |
| glossi | 0.008 | 0.019 | 0.026 | |
| glossiMarginal | 0.003 | 0.001 | 0.004 | |
| pValue-method | 0.000 | 0.000 | 0.001 | |
| simulatedStats-method | 0 | 0 | 0 | |
| statistic-methods | 0 | 0 | 0 | |