Welliton Souza
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/Rqc |
| Branch: RELEASE_3_6 |
| Last Commit: 7abec5a |
| Last Changed Date: 2017-10-30 12:40:45 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:48 -0400 (Thu, 12 Apr 2018).
| Package 1211/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rqc 1.12.0 Welliton Souza
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: Rqc |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rqc_1.12.0.tar.gz |
| StartedAt: 2018-04-12 09:01:03 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 09:07:04 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 361.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rqc.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rqc_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Rqc.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 ‘Rqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rqc’ 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rqc’ 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 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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
Rqc-package 18.949 0.666 20.443
rqc 14.417 0.512 15.628
rqcReport 9.550 0.387 10.361
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/Rqc.Rcheck/00check.log’
for details.
Rqc.Rcheck/00install.out
* installing *source* package ‘Rqc’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RRDNA.cpp -o RRDNA.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.6-bioc/meat/Rqc.Rcheck/Rqc/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rqc)
Rqc.Rcheck/tests/testthat.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.
> library(testthat)
> library(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
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, 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
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following object is masked from 'package:base':
apply
Loading required package: ggplot2
>
> test_check("Rqc")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 27 SKIPPED: 0 FAILED: 0
Warning message:
In .Internal(sys.parent(n)) :
closing unused connection 3 (/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
>
> proc.time()
user system elapsed
16.723 0.573 17.869
Rqc.Rcheck/Rqc-Ex.timings
| name | user | system | elapsed | |
| Rqc-package | 18.949 | 0.666 | 20.443 | |
| RqcResultSet-class | 0.046 | 0.002 | 0.048 | |
| checkpoint | 0.004 | 0.001 | 0.004 | |
| detectFileFormat | 0.003 | 0.000 | 0.003 | |
| fromRRDNA | 0.001 | 0.000 | 0.002 | |
| matdist | 0.001 | 0.000 | 0.001 | |
| rqc | 14.417 | 0.512 | 15.628 | |
| rqcCycleAverageQualityPcaPlot | 0.326 | 0.002 | 0.336 | |
| rqcCycleAverageQualityPlot | 0.372 | 0.003 | 0.385 | |
| rqcCycleBaseCallsPlot | 0.613 | 0.003 | 0.641 | |
| rqcCycleGCPlot | 0.336 | 0.001 | 0.346 | |
| rqcCycleQualityBoxPlot | 3.295 | 0.008 | 3.373 | |
| rqcCycleQualityPlot | 1.128 | 0.018 | 1.182 | |
| rqcFileHeatmap | 0.189 | 0.001 | 0.192 | |
| rqcGroupCycleAverageQualityPlot | 0.320 | 0.001 | 0.326 | |
| rqcQA | 0.225 | 0.001 | 0.229 | |
| rqcReadFrequencyPlot | 0.209 | 0.001 | 0.212 | |
| rqcReadQualityBoxPlot | 0.272 | 0.001 | 0.276 | |
| rqcReadQualityPlot | 0.207 | 0.001 | 0.210 | |
| rqcReadWidthPlot | 0.271 | 0.001 | 0.278 | |
| rqcReport | 9.550 | 0.387 | 10.361 | |
| rqcShinyReport | 0.003 | 0.000 | 0.004 | |
| stats4trim | 0.136 | 0.003 | 0.141 | |
| subsetByGroup | 1.665 | 0.062 | 1.758 | |
| subsetByPair | 0.008 | 0.000 | 0.009 | |
| toRRDNA | 0.001 | 0.000 | 0.002 | |