Tom Carroll
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/soGGi |
| Branch: master |
| Last Commit: b64fd3b |
| Last Changed Date: 2019-03-27 18:59:15 -0400 (Wed, 27 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:13:58 -0400 (Tue, 09 Apr 2019).
| Package 1524/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| soGGi 1.15.1 Tom Carroll
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: soGGi |
| Version: 1.15.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:soGGi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings soGGi_1.15.1.tar.gz |
| StartedAt: 2019-04-09 05:39:52 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:46:10 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 378.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: soGGi.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:soGGi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings soGGi_1.15.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/soGGi.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘soGGi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘soGGi’ version ‘1.15.1’
* 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 ‘soGGi’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/soGGi.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 ... NOTE
Foreign function call to a different package:
.Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
plotCuts: warning in ggsave(myP, file = outName): partial argument
match of 'file' to 'filename'
GetGRanges: no visible global function definition for ‘read.delim’
GetGRanges: possible error in `seqlevels<-`(RegionRanges, force = TRUE,
value = `*tmpv*`): unused argument (force = TRUE)
findconsensusRegions : <anonymous>: no visible global function
definition for ‘weighted.mean’
getShifts: no visible global function definition for
‘readGAlignmentsFromBam’
getSummitScore: no visible global function definition for
‘readGAlignmentsFromBam’
plotHeatmap: no visible global function definition for ‘heat.colors’
plotHeatmap: no visible global function definition for ‘layout’
plotHeatmap: no visible global function definition for ‘par’
plotRegion.ChIPprofile: no visible global function definition for
‘formula’
runFindSummit: no visible global function definition for
‘readGAlignmentsFromBam’
runRegionPlot : <anonymous>: no visible global function definition for
‘spline’
summitPipeline: no visible global function definition for
‘readGAlignmentsFromBam’
plotRegion,ChIPprofile: no visible global function definition for
‘formula’
Undefined global functions or variables:
formula heat.colors layout par read.delim readGAlignmentsFromBam
spline weighted.mean
Consider adding
importFrom("grDevices", "heat.colors")
importFrom("graphics", "layout", "par")
importFrom("stats", "formula", "spline", "weighted.mean")
importFrom("utils", "read.delim")
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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/soGGi.Rcheck/00check.log’
for details.
soGGi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL soGGi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘soGGi’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’ ** help *** installing help indices ** building package indices ** installing vignettes ‘soggi.Rnw’ ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’ ** testing if installed package keeps a record of temporary installation path * DONE (soGGi)
soGGi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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.
> library(testthat)
> library(soGGi)
Loading required package: BiocGenerics
Loading required package: parallel
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, 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
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
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
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
>
> test_check("soGGi")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
17.692 1.419 19.063
soGGi.Rcheck/soGGi-Ex.timings
| name | user | system | elapsed | |
| ChIPprofile | 0.304 | 0.031 | 0.336 | |
| Ops | 0.755 | 0.055 | 0.810 | |
| groupByOverlaps | 0.661 | 0.036 | 0.697 | |
| manipulateObjects | 0.895 | 0.050 | 0.946 | |
| normalise | 1.513 | 0.159 | 1.658 | |
| normaliseQuantiles | 0.737 | 0.138 | 0.864 | |
| orientBy | 0.354 | 0.016 | 0.369 | |
| plotRegion | 0.699 | 0.028 | 0.728 | |
| pwmToCoverage | 0.005 | 0.012 | 0.018 | |