Welliton Souza
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rqc |
| Branch: master |
| Last Commit: b6bcc59 |
| Last Changed Date: 2019-03-01 14:32:02 -0400 (Fri, 01 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:40:18 -0400 (Tue, 09 Apr 2019).
| Package 1388/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rqc 1.17.3 Welliton Souza
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: Rqc |
| Version: 1.17.3 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rqc_1.17.3.tar.gz |
| StartedAt: 2019-04-09 03:20:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:26:12 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 355.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rqc.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rqc_1.17.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rqc.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.17.3’
* package encoding: UTF-8
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'IRanges' 'Rcpp'
All declared Imports should be used.
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Rqc-package 11.199 0.219 11.470
rqc 10.918 0.212 11.132
rqcReport 10.081 0.072 10.154
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/Rqc.Rcheck/00check.log’
for details.
Rqc.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rqc
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Rqc’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function ‘Rcpp::StringVector toRRDNA(Rcpp::StringVector)’:
RRDNA.cpp:51:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j < dna.size(); j+=3)
˜˜^˜˜˜˜˜˜˜˜˜˜˜
RRDNA.cpp: In function ‘Rcpp::StringVector fromRRDNA(Rcpp::StringVector)’:
RRDNA.cpp:102:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j = 1; j < rrdna.size(); ++j) {
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-Rqc/00new/Rqc/libs
** R
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rqc)
Rqc.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-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)
> 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, 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: 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 objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: ggplot2
>
> test_check("Rqc")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 27 SKIPPED: 0 FAILED: 0
Warning messages:
1: In getClassDef(class1) :
closing unused connection 5 (/home/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In getClassDef(class1) :
closing unused connection 4 (/home/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
>
> proc.time()
user system elapsed
19.103 0.586 19.695
Rqc.Rcheck/Rqc-Ex.timings
| name | user | system | elapsed | |
| Rqc-package | 11.199 | 0.219 | 11.470 | |
| RqcResultSet-class | 0.039 | 0.000 | 0.167 | |
| checkpoint | 0.004 | 0.000 | 0.003 | |
| detectFileFormat | 0.004 | 0.001 | 0.005 | |
| fromRRDNA | 0.000 | 0.001 | 0.001 | |
| matdist | 0.000 | 0.000 | 0.001 | |
| rqc | 10.918 | 0.212 | 11.132 | |
| rqcCycleAverageQualityPcaPlot | 0.228 | 0.000 | 0.227 | |
| rqcCycleAverageQualityPlot | 0.317 | 0.000 | 0.317 | |
| rqcCycleBaseCallsPlot | 0.763 | 0.000 | 0.775 | |
| rqcCycleGCPlot | 0.283 | 0.000 | 0.282 | |
| rqcCycleQualityBoxPlot | 3.072 | 0.000 | 3.073 | |
| rqcCycleQualityPlot | 0.905 | 0.000 | 0.905 | |
| rqcFileHeatmap | 0.177 | 0.000 | 0.177 | |
| rqcGroupCycleAverageQualityPlot | 0.281 | 0.004 | 0.285 | |
| rqcQA | 0.207 | 0.000 | 0.207 | |
| rqcReadFrequencyPlot | 0.315 | 0.000 | 0.315 | |
| rqcReadQualityBoxPlot | 0.423 | 0.000 | 0.427 | |
| rqcReadQualityPlot | 0.336 | 0.000 | 0.336 | |
| rqcReadWidthPlot | 0.326 | 0.000 | 0.326 | |
| rqcReport | 10.081 | 0.072 | 10.154 | |
| rqcShinyReport | 0.000 | 0.004 | 0.005 | |
| stats4trim | 0.083 | 0.008 | 0.090 | |
| subsetByGroup | 0.535 | 0.008 | 0.544 | |
| subsetByPair | 0.004 | 0.000 | 0.005 | |
| toRRDNA | 0.001 | 0.000 | 0.001 | |