Jack Fu
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ballgown |
| Branch: RELEASE_3_8 |
| Last Commit: aa95afd |
| Last Changed Date: 2019-01-04 13:19:35 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:42 -0400 (Tue, 16 Apr 2019).
| Package 95/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ballgown 2.14.1 Jack Fu
| 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: ballgown |
| Version: 2.14.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ballgown.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ballgown_2.14.1.tar.gz |
| StartedAt: 2019-04-15 22:18:59 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:25:32 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 392.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ballgown.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ballgown.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ballgown_2.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ballgown.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.14.1’
* 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 ‘ballgown’ 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
.readExon: no visible global function definition for ‘read.table’
.readIntron: no visible global function definition for ‘read.table’
.readTranscript: no visible global function definition for ‘read.table’
assessSim: no visible global function definition for ‘read.table’
assessSim: no visible global function definition for ‘lines’
assessSim: no visible global function definition for ‘legend’
ballgown: no visible global function definition for ‘read.table’
ballgownrsem: no visible global function definition for ‘read.table’
ballgownrsem : <anonymous>: no visible global function definition for
‘read.table’
checkAssembledTx: no visible global function definition for ‘par’
checkAssembledTx: no visible global function definition for ‘plot’
checkAssembledTx: no visible global function definition for ‘polygon’
checkAssembledTx: no visible global function definition for ‘lines’
checkAssembledTx: no visible global function definition for ‘abline’
checkAssembledTx: no visible global function definition for ‘title’
checkAssembledTx: no visible global function definition for ‘axis’
closestColor: no visible global function definition for ‘heat.colors’
clusterTranscripts: no visible global function definition for ‘cutree’
clusterTranscripts: no visible global function definition for ‘hclust’
clusterTranscripts: no visible global function definition for ‘as.dist’
clusterTranscripts: no visible global function definition for ‘kmeans’
gffRead: no visible global function definition for ‘read.table’
plotMeans: no visible global function definition for ‘par’
plotMeans: no visible global function definition for ‘plot’
plotMeans: no visible global function definition for ‘polygon’
plotMeans: no visible global function definition for ‘lines’
plotMeans: no visible global function definition for ‘heat.colors’
plotMeans: no visible global function definition for ‘text’
plotMeans: no visible global function definition for ‘axis’
plotTranscripts: no visible global function definition for ‘par’
plotTranscripts: no visible global function definition for ‘plot’
plotTranscripts: no visible global function definition for ‘title’
plotTranscripts: no visible global function definition for ‘polygon’
plotTranscripts: no visible global function definition for ‘lines’
plotTranscripts: no visible global function definition for
‘heat.colors’
plotTranscripts: no visible global function definition for ‘text’
plotTranscripts: no visible global function definition for ‘axis’
stattest: no visible global function definition for ‘model.matrix’
stattest: no visible global function definition for ‘p.adjust’
writeFiles: no visible global function definition for ‘write.table’
subset,ballgown: no visible binding for global variable ‘i_id’
subset,ballgown: no visible binding for global variable ‘e_id’
subset,ballgown: no visible binding for global variable ‘t_id’
Undefined global functions or variables:
abline as.dist axis cutree e_id hclust heat.colors i_id kmeans legend
lines model.matrix p.adjust par plot polygon read.table t_id text
title write.table
Consider adding
importFrom("grDevices", "heat.colors")
importFrom("graphics", "abline", "axis", "legend", "lines", "par",
"plot", "polygon", "text", "title")
importFrom("stats", "as.dist", "cutree", "hclust", "kmeans",
"model.matrix", "p.adjust")
importFrom("utils", "read.table", "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
annotate_assembly 27.456 0.088 27.627
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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
‘/home/biocbuild/bbs-3.8-bioc/meat/ballgown.Rcheck/00check.log’
for details.
ballgown.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ballgown ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘ballgown’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘structure’ in package ‘ballgown’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ballgown)
ballgown.Rcheck/tests/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
> test_check('ballgown')
Loading required package: ballgown
Attaching package: 'ballgown'
The following object is masked from 'package:base':
structure
══ testthat results ═══════════════════════════════════════════════════════════
OK: 178 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
121.260 0.564 122.972
ballgown.Rcheck/ballgown-Ex.timings
| name | user | system | elapsed | |
| annotate_assembly | 27.456 | 0.088 | 27.627 | |
| ballgown-class | 0.072 | 0.000 | 0.072 | |
| ballgown-constructor | 0.288 | 0.020 | 0.572 | |
| ballgownrsem | 3.396 | 0.024 | 3.532 | |
| bg | 0.040 | 0.004 | 0.043 | |
| checkAssembledTx | 0 | 0 | 0 | |
| clusterTranscripts | 0.400 | 0.000 | 0.398 | |
| collapseTranscripts | 0.428 | 0.000 | 0.429 | |
| dirs | 0.040 | 0.004 | 0.046 | |
| eexpr | 0.044 | 0.000 | 0.047 | |
| expr-replace | 0.072 | 0.000 | 0.073 | |
| expr | 0.040 | 0.004 | 0.044 | |
| exprfilter | 0.064 | 0.004 | 0.066 | |
| geneIDs | 0.044 | 0.000 | 0.045 | |
| geneNames | 0.476 | 0.008 | 0.483 | |
| getAttributeField | 1.592 | 0.004 | 1.597 | |
| getGenes | 0.364 | 0.000 | 0.365 | |
| gexpr | 0.144 | 0.000 | 0.143 | |
| gffRead | 0.168 | 0.000 | 0.166 | |
| gffReadGR | 0.448 | 0.000 | 0.448 | |
| iexpr | 0.048 | 0.000 | 0.046 | |
| indexes-replace | 0.044 | 0.000 | 0.046 | |
| indexes | 0.044 | 0.000 | 0.046 | |
| last | 0.004 | 0.000 | 0.001 | |
| mergedDate | 0.044 | 0.000 | 0.044 | |
| pData-replace | 0.044 | 0.004 | 0.046 | |
| pData | 0.044 | 0.000 | 0.045 | |
| pctOverlap | 0.364 | 0.000 | 0.365 | |
| plotLatentTranscripts | 0 | 0 | 0 | |
| plotMeans | 0.000 | 0.000 | 0.001 | |
| plotTranscripts | 0 | 0 | 0 | |
| sampleNames | 0.044 | 0.000 | 0.044 | |
| seqnames | 0.048 | 0.000 | 0.044 | |
| stattest | 0.860 | 0.004 | 0.868 | |
| structure | 0.06 | 0.00 | 0.06 | |
| subset | 0.236 | 0.000 | 0.240 | |
| tGene | 0.048 | 0.000 | 0.050 | |
| texpr | 0.044 | 0.000 | 0.044 | |
| transcriptIDs | 0.036 | 0.008 | 0.044 | |
| transcriptNames | 0.044 | 0.000 | 0.045 | |
| writeFiles | 0 | 0 | 0 | |