Welliton Souza
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Rqc |
| Branch: RELEASE_3_7 |
| Last Commit: 029044f |
| Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:26:56 -0400 (Wed, 17 Oct 2018).
| Package 1276/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rqc 1.14.0 Welliton Souza
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rqc |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Rqc_1.14.0.tar.gz |
| StartedAt: 2018-10-16 03:25:27 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 03:29:52 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 265.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rqc.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Rqc_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 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 ... 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 10.308 0.116 10.559
rqc 9.140 0.164 9.311
rqcReport 8.648 0.044 8.701
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck/00check.log’
for details.
Rqc.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL Rqc
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘Rqc’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (Rqc)
Rqc.Rcheck/tests/testthat.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-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, 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 objects are masked from 'package:base':
aperm, apply
Loading required package: ggplot2
>
> test_check("Rqc")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 27 SKIPPED: 0 FAILED: 0
Warning messages:
1: In callNextMethod() :
closing unused connection 3 (/home/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In callNextMethod() :
closing unused connection 4 (/home/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
>
> proc.time()
user system elapsed
14.392 0.352 14.758
Rqc.Rcheck/Rqc-Ex.timings
| name | user | system | elapsed | |
| Rqc-package | 10.308 | 0.116 | 10.559 | |
| RqcResultSet-class | 0.032 | 0.000 | 0.044 | |
| checkpoint | 0.004 | 0.000 | 0.003 | |
| detectFileFormat | 0.004 | 0.000 | 0.003 | |
| fromRRDNA | 0.004 | 0.000 | 0.001 | |
| matdist | 0.000 | 0.000 | 0.001 | |
| rqc | 9.140 | 0.164 | 9.311 | |
| rqcCycleAverageQualityPcaPlot | 0.264 | 0.000 | 0.263 | |
| rqcCycleAverageQualityPlot | 0.324 | 0.000 | 0.324 | |
| rqcCycleBaseCallsPlot | 0.528 | 0.000 | 0.525 | |
| rqcCycleGCPlot | 0.260 | 0.004 | 0.265 | |
| rqcCycleQualityBoxPlot | 2.076 | 0.000 | 2.078 | |
| rqcCycleQualityPlot | 0.748 | 0.000 | 0.753 | |
| rqcFileHeatmap | 0.188 | 0.004 | 0.193 | |
| rqcGroupCycleAverageQualityPlot | 0.304 | 0.000 | 0.304 | |
| rqcQA | 0.228 | 0.000 | 0.229 | |
| rqcReadFrequencyPlot | 0.236 | 0.000 | 0.238 | |
| rqcReadQualityBoxPlot | 0.256 | 0.000 | 0.255 | |
| rqcReadQualityPlot | 0.212 | 0.000 | 0.211 | |
| rqcReadWidthPlot | 0.248 | 0.000 | 0.246 | |
| rqcReport | 8.648 | 0.044 | 8.701 | |
| rqcShinyReport | 0.000 | 0.004 | 0.004 | |
| stats4trim | 0.072 | 0.000 | 0.072 | |
| subsetByGroup | 1.264 | 0.204 | 1.468 | |
| subsetByPair | 0.000 | 0.004 | 0.006 | |
| toRRDNA | 0.000 | 0.000 | 0.001 | |