Nicolas Delhomme
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/easyRNASeq |
| Branch: RELEASE_3_7 |
| Last Commit: 09fe48d |
| Last Changed Date: 2018-04-30 10:35:23 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:24:06 -0400 (Wed, 17 Oct 2018).
| Package 423/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| easyRNASeq 2.16.0 Nicolas Delhomme
| 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: easyRNASeq |
| Version: 2.16.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings easyRNASeq_2.16.0.tar.gz |
| StartedAt: 2018-10-16 00:03:17 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:08:58 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 340.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: easyRNASeq.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:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings easyRNASeq_2.16.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/easyRNASeq.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 ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
‘inst/doc/01-Introduction.Rmd’
‘inst/doc/02-AnnotParam.Rmd’
‘inst/doc/03-SyntheticTranscripts.Rmd’
‘inst/doc/04-BamParam.Rmd’
‘inst/doc/05-RnaSeqParam.Rmd’
‘inst/doc/06-simpleRNASeq.Rmd’
‘inst/doc/08-Session-Info.Rmd’
‘inst/doc/09-Acknowledgments.Rmd’
‘inst/doc/10-Foonotes.Rmd’
‘inst/doc/11-Images.Rmd’
‘inst/doc/12-Appendix.Rmd’
(Is a VignetteBuilder field missing?)
* 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 ‘easyRNASeq’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
easyRNASeq-package 36.448 0.440 49.562
easyRNASeq-synthetic-transcripts 28.356 0.136 30.426
easyRNASeq-simpleRNASeq 26.360 0.244 32.370
Rsamtools-methods 0.328 0.076 6.433
easyRNASeq-BamFileList 0.124 0.024 5.482
* 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
‘/home/biocbuild/bbs-3.7-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.
easyRNASeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL easyRNASeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘easyRNASeq’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’ Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (easyRNASeq)
easyRNASeq.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-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.
> # get the example data and annotation files from GitHub using curl
> library(curl)
> exFiles <- c("gAnnot.rda",
+ "Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz",
+ "Dmel-mRNA-exon-r5.52.gff3.gz",
+ "ACACTG.bam","ACTAGC.bam","ATGGCT.bam","TTGCGA.bam",
+ "ACACTG.bam.bai","ACTAGC.bam.bai","ATGGCT.bam.bai","TTGCGA.bam.bai")
>
> invisible(sapply(exFiles,function(f){
+ if(!file.exists(f)){
+ invisible(curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
+ "master/tutorial/easyRNASeq/",f),f))
+ }
+ }))
>
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
Loading required package: stats4
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 object is masked from 'package:easyRNASeq':
basename
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
No validation performed at that stage
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 1000 records
Validated a datasource of type gtf
Read 999 records
Validated a datasource of type gff3
RUNIT TEST PROTOCOL -- Tue Oct 16 00:08:53 2018
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
easyRNASeq RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning messages:
1: In FUN(X[[i]], ...) : Bam file: ACACTG.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
Bam file: ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded.
3: In FUN(X[[i]], ...) : Bam file: ACTAGC.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
Bam file: ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded.
5: In FUN(X[[i]], ...) : Bam file: ATGGCT.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
Bam file: ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded.
7: In FUN(X[[i]], ...) : Bam file: TTGCGA.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
Bam file: TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded.
9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
You provided an incorrect BAM parameter; 'paired' should be set to 'FALSE'.
10: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
As of version 2.15.5, easyRNASeq assumes that, if the data is strand specific, the sequencing was done using a protocol such as the Illumina TruSeq, where the reverse strand is quantified - i.e. the strandProtocol argument of the BamParam class defaults to 'reverse'.
>
> # cleanup
> file.remove(exFiles)
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
> proc.time()
user system elapsed
25.476 0.620 37.026
easyRNASeq.Rcheck/easyRNASeq-Ex.timings
| name | user | system | elapsed | |
| DESeq-methods | 0.000 | 0.000 | 0.002 | |
| GenomicRanges-methods | 0.352 | 0.008 | 0.360 | |
| IRanges-methods | 0 | 0 | 0 | |
| Rsamtools-methods | 0.328 | 0.076 | 6.433 | |
| ShortRead-methods | 0.004 | 0.000 | 0.002 | |
| easyRNASeq-AnnotParam-accessors | 0.032 | 0.016 | 2.769 | |
| easyRNASeq-AnnotParam-class | 0.000 | 0.000 | 0.002 | |
| easyRNASeq-AnnotParam | 0.028 | 0.000 | 0.936 | |
| easyRNASeq-BamFileList | 0.124 | 0.024 | 5.482 | |
| easyRNASeq-BamParam-accessors | 0.000 | 0.000 | 0.002 | |
| easyRNASeq-BamParam-class | 0.000 | 0.000 | 0.001 | |
| easyRNASeq-BamParam | 0.000 | 0.000 | 0.003 | |
| easyRNASeq-RnaSeqParam-accessors | 0.008 | 0.000 | 0.009 | |
| easyRNASeq-RnaSeqParam-class | 0.004 | 0.000 | 0.002 | |
| easyRNASeq-RnaSeqParam | 0.004 | 0.000 | 0.005 | |
| easyRNASeq-accessors | 0.004 | 0.000 | 0.001 | |
| easyRNASeq-annotation-methods | 0.000 | 0.000 | 0.001 | |
| easyRNASeq-class | 0.004 | 0.000 | 0.002 | |
| easyRNASeq-correction-methods | 0.000 | 0.000 | 0.001 | |
| easyRNASeq-coverage-methods | 0.000 | 0.000 | 0.001 | |
| easyRNASeq-easyRNASeq | 0.000 | 0.000 | 0.002 | |
| easyRNASeq-island-methods | 0.000 | 0.000 | 0.001 | |
| easyRNASeq-package | 36.448 | 0.440 | 49.562 | |
| easyRNASeq-simpleRNASeq | 26.360 | 0.244 | 32.370 | |
| easyRNASeq-summarization-methods | 0.004 | 0.000 | 0.001 | |
| easyRNASeq-synthetic-transcripts | 28.356 | 0.136 | 30.426 | |
| edgeR-methods | 0.004 | 0.000 | 0.001 | |
| genomeIntervals-methods | 1.152 | 0.016 | 1.892 | |
| parallel-methods | 0.000 | 0.000 | 0.001 | |