Oscar Krijgsman
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/focalCall |
| Branch: RELEASE_3_6 |
| Last Commit: 7ccdb60 |
| Last Changed Date: 2017-10-30 12:40:42 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:35 -0400 (Thu, 12 Apr 2018).
| Package 502/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| focalCall 1.12.0 Oscar Krijgsman
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: focalCall |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings focalCall_1.12.0.tar.gz |
| StartedAt: 2018-04-12 03:52:47 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:53:43 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 55.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: focalCall.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings focalCall_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/focalCall.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘focalCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘focalCall’ version ‘1.12.0’
* 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 ‘focalCall’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... 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
.match_CNV2CGH: no visible global function definition for ‘bpstart’
.match_CNV2CGH: no visible global function definition for ‘chromosomes’
.match_CNV2CGH: no visible global function definition for ‘bpend’
FreqPlot: no visible global function definition for ‘chromosomes’
FreqPlot: no visible global function definition for ‘plot’
FreqPlot: no visible global function definition for ‘points’
FreqPlot: no visible global function definition for ‘abline’
FreqPlot: no visible global function definition for ‘axis’
FreqPlotfocal: no visible global function definition for ‘chromosomes’
FreqPlotfocal: no visible global function definition for
‘assayDataElement’
FreqPlotfocal: no visible global function definition for ‘fData’
FreqPlotfocal: no visible global function definition for ‘plot’
FreqPlotfocal: no visible global function definition for ‘points’
FreqPlotfocal: no visible global function definition for ‘abline’
FreqPlotfocal: no visible global function definition for ‘axis’
focalCall: no visible global function definition for ‘calls’
focalCall: no visible global function definition for ‘featureNames’
focalCall: no visible global function definition for ‘segmented’
focalCall: no visible global function definition for ‘chromosomes’
focalCall: no visible global function definition for ‘bpstart’
focalCall: no visible global function definition for
‘assayDataElement<-’
focalCall: no visible global function definition for ‘assayDataElement’
focalCall: no visible global function definition for ‘bpend’
focalCall: no visible global function definition for ‘fData’
focalCall: no visible global function definition for ‘fData<-’
focalCall: no visible global function definition for ‘write.table’
igvFiles: no visible global function definition for ‘calls’
igvFiles: no visible global function definition for ‘chromosomes’
igvFiles: no visible global function definition for ‘bpstart’
igvFiles: no visible global function definition for ‘bpend’
igvFiles: no visible global function definition for ‘featureNames’
igvFiles: no visible global function definition for ‘segmented’
igvFiles: no visible global function definition for ‘write.table’
igvFiles: no visible global function definition for ‘assayDataElement’
singleSample: no visible global function definition for ‘calls’
singleSample: no visible global function definition for ‘featureNames’
singleSample: no visible global function definition for ‘fData’
singleSample: no visible global function definition for ‘fData<-’
singleSample: no visible global function definition for
‘assayDataElement<-’
singleSample: no visible global function definition for ‘segmented’
singleSample: no visible global function definition for ‘chromosomes’
singleSample: no visible global function definition for ‘bpend’
singleSample: no visible global function definition for ‘bpstart’
singleSample: no visible global function definition for
‘assayDataElement’
singleSample: no visible global function definition for ‘median’
singleSample: no visible global function definition for ‘png’
singleSample: no visible global function definition for ‘plot’
singleSample: no visible global function definition for ‘dev.off’
singleSample: no visible global function definition for ‘write.table’
Undefined global functions or variables:
abline assayDataElement assayDataElement<- axis bpend bpstart calls
chromosomes dev.off fData fData<- featureNames median plot png points
segmented write.table
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "abline", "axis", "plot", "points")
importFrom("stats", "median")
importFrom("utils", "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
focalCall 5.173 0.098 5.343
* 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-3.6-bioc/meat/focalCall.Rcheck/00check.log’
for details.
focalCall.Rcheck/00install.out
* installing *source* package ‘focalCall’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (focalCall)
focalCall.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("focalCall")
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, cbind, colMeans, colSums, colnames, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Attaching package: 'snow'
The following objects are masked from 'package:BiocGenerics':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, parApply, parCapply,
parLapply, parRapply, parSapply
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster
Attaching package: 'CGHcall'
The following object is masked from 'package:BiocGenerics':
normalize
RUNIT TEST PROTOCOL -- Thu Apr 12 03:53:39 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
focalCall RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.286 0.072 1.357
focalCall.Rcheck/focalCall-Ex.timings
| name | user | system | elapsed | |
| BierkensCNA | 0.542 | 0.032 | 0.590 | |
| FreqPlot | 0.494 | 0.030 | 0.541 | |
| FreqPlotfocal | 0.708 | 0.030 | 0.752 | |
| focalCall | 5.173 | 0.098 | 5.343 | |
| igvFiles | 1.544 | 0.061 | 1.622 | |
| singleSample | 2.437 | 0.091 | 2.584 | |