Gabriela Merino
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TarSeqQC |
| Branch: RELEASE_3_8 |
| Last Commit: 5a68300 |
| Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:59 -0400 (Tue, 16 Apr 2019).
| Package 1544/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TarSeqQC 1.12.0 Gabriela Merino
| 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: TarSeqQC |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TarSeqQC_1.12.0.tar.gz |
| StartedAt: 2019-04-16 03:04:56 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:09:25 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 269.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TarSeqQC.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TarSeqQC_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/TarSeqQC.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 ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ 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 ‘TarSeqQC’ 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
plotNtdPercentage,TargetExperiment: no visible global function
definition for ‘path’
plotRegion,TargetExperiment: no visible global function definition for
‘path’
readFrequencies,TargetExperiment: no visible global function definition
for ‘path’
Undefined global functions or variables:
path
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
TargetExperiment-class 20.756 8.535 15.728
TargetExperiment-plotRegion 6.200 2.455 2.967
* 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-3.8-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.
TarSeqQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TarSeqQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘TarSeqQC’ ... ** 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 (TarSeqQC)
TarSeqQC.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("TarSeqQC")
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
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
RUNIT TEST PROTOCOL -- Tue Apr 16 03:09:18 2019
***********************************************
Number of test functions: 33
Number of errors: 0
Number of failures: 0
1 Test Suite :
TarSeqQC RUnit Tests - 33 test functions, 0 errors, 0 failures
Number of test functions: 33
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
19.627 4.729 19.045
TarSeqQC.Rcheck/TarSeqQC-Ex.timings
| name | user | system | elapsed | |
| TargetExperiment-biasExploration | 0.097 | 0.004 | 0.101 | |
| TargetExperiment-buildFeaturePanel | 1.193 | 0.044 | 1.259 | |
| TargetExperiment-buildReport | 2.212 | 0.056 | 2.299 | |
| TargetExperiment-class | 20.756 | 8.535 | 15.728 | |
| TargetExperiment-constructor | 2.698 | 1.326 | 2.230 | |
| TargetExperiment-getters | 0.268 | 0.048 | 0.319 | |
| TargetExperiment-initialize | 0.003 | 0.000 | 0.003 | |
| TargetExperiment-plot | 0.431 | 0.056 | 0.490 | |
| TargetExperiment-plotAttrExpl | 0.115 | 0.009 | 0.123 | |
| TargetExperiment-plotAttrPerform | 0.041 | 0.006 | 0.047 | |
| TargetExperiment-plotFeatPerform | 0.633 | 0.009 | 0.649 | |
| TargetExperiment-plotFeature | 0.689 | 0.642 | 0.724 | |
| TargetExperiment-plotGeneAttrPerFeat | 0.626 | 0.073 | 0.709 | |
| TargetExperiment-plotMetaDataExpl | 0.046 | 0.008 | 0.057 | |
| TargetExperiment-plotNtdPercentage | 0.596 | 0.537 | 0.578 | |
| TargetExperiment-plotRegion | 6.200 | 2.455 | 2.967 | |
| TargetExperiment-print | 0.054 | 0.023 | 0.080 | |
| TargetExperiment-readFrequencies | 0.639 | 0.374 | 0.710 | |
| TargetExperiment-setters | 0.006 | 0.004 | 0.009 | |
| TargetExperiment-show | 0.047 | 0.015 | 0.062 | |
| TargetExperiment-statistics | 0.071 | 0.016 | 0.087 | |
| TargetExperiment-summarizePanel | 1.091 | 0.759 | 0.588 | |
| TargetExperimentList-class | 0.753 | 0.107 | 0.869 | |
| TargetExperimentList-constructor | 0.080 | 0.017 | 0.100 | |
| TargetExperimentList-initialize | 0.056 | 0.010 | 0.066 | |
| TargetExperimentList-plotGlobalAttrExpl | 0.035 | 0.007 | 0.041 | |
| TargetExperimentList-plotPoolPerformance | 0.018 | 0.010 | 0.028 | |
| checkBedFasta | 0.047 | 0.001 | 0.049 | |
| pileupCounts | 1.216 | 1.366 | 1.030 | |
| plotInOutFeatures | 0.641 | 0.417 | 0.711 | |