Gabriela Merino
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/TarSeqQC |
| Branch: RELEASE_3_7 |
| Last Commit: 657e2d3 |
| Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:55:23 -0400 (Wed, 17 Oct 2018).
| Package 1465/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TarSeqQC 1.10.0 Gabriela Merino
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: TarSeqQC |
| Version: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2018-10-17 00:22:39 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:27:04 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 264.7 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ... NOTE
Error in .requirePackage(package) :
unable to find required package 'TarSeqQC'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* 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 20.458 7.422 16.055
TargetExperiment-plotRegion 7.093 2.709 3.467
* 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-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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("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 -- Wed Oct 17 00:26:56 2018
***********************************************
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
19.467 4.538 18.974
TarSeqQC.Rcheck/TarSeqQC-Ex.timings
| name | user | system | elapsed | |
| TargetExperiment-biasExploration | 0.060 | 0.006 | 0.066 | |
| TargetExperiment-buildFeaturePanel | 1.315 | 0.044 | 1.373 | |
| TargetExperiment-buildReport | 1.382 | 0.044 | 1.430 | |
| TargetExperiment-class | 20.458 | 7.422 | 16.055 | |
| TargetExperiment-constructor | 2.495 | 0.712 | 2.076 | |
| TargetExperiment-getters | 0.300 | 0.058 | 0.360 | |
| TargetExperiment-initialize | 0.005 | 0.000 | 0.005 | |
| TargetExperiment-plot | 0.497 | 0.069 | 0.575 | |
| TargetExperiment-plotAttrExpl | 0.171 | 0.018 | 0.189 | |
| TargetExperiment-plotAttrPerform | 0.044 | 0.008 | 0.053 | |
| TargetExperiment-plotFeatPerform | 0.750 | 0.011 | 0.770 | |
| TargetExperiment-plotFeature | 0.965 | 0.863 | 0.904 | |
| TargetExperiment-plotGeneAttrPerFeat | 0.807 | 0.086 | 0.904 | |
| TargetExperiment-plotMetaDataExpl | 0.036 | 0.008 | 0.045 | |
| TargetExperiment-plotNtdPercentage | 0.919 | 1.029 | 0.825 | |
| TargetExperiment-plotRegion | 7.093 | 2.709 | 3.467 | |
| TargetExperiment-print | 0.061 | 0.020 | 0.080 | |
| TargetExperiment-readFrequencies | 0.546 | 0.382 | 0.619 | |
| TargetExperiment-setters | 0.008 | 0.006 | 0.015 | |
| TargetExperiment-show | 0.056 | 0.019 | 0.076 | |
| TargetExperiment-statistics | 0.082 | 0.024 | 0.105 | |
| TargetExperiment-summarizePanel | 1.104 | 0.805 | 0.627 | |
| TargetExperimentList-class | 0.717 | 0.114 | 0.837 | |
| TargetExperimentList-constructor | 0.051 | 0.009 | 0.060 | |
| TargetExperimentList-initialize | 0.052 | 0.009 | 0.061 | |
| TargetExperimentList-plotGlobalAttrExpl | 0.022 | 0.004 | 0.027 | |
| TargetExperimentList-plotPoolPerformance | 0.012 | 0.003 | 0.016 | |
| checkBedFasta | 0.034 | 0.001 | 0.035 | |
| pileupCounts | 0.821 | 0.683 | 0.663 | |
| plotInOutFeatures | 0.572 | 0.338 | 0.667 | |