Nicolas Delhomme
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/easyRNASeq |
| Branch: RELEASE_3_8 |
| Last Commit: 0931ba8 |
| Last Changed Date: 2019-04-13 16:06:10 -0400 (Sat, 13 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:12 -0400 (Tue, 16 Apr 2019).
| Package 447/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| easyRNASeq 2.18.4 Nicolas Delhomme
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: easyRNASeq |
| Version: 2.18.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings easyRNASeq_2.18.4.tar.gz |
| StartedAt: 2019-04-15 23:41:22 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:51:13 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 591.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: easyRNASeq.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings easyRNASeq_2.18.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.18.4’
* package encoding: UTF-8
* 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 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
easyRNASeq-simpleRNASeq 96.306 2.055 103.014
easyRNASeq-package 70.568 1.738 75.573
easyRNASeq-synthetic-transcripts 59.888 1.533 63.289
* 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
‘/Users/biocbuild/bbs-3.8-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.
easyRNASeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL easyRNASeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘easyRNASeq’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘rev’ when loading ‘easyRNASeq’ 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 No methods found in package ‘IRanges’ for request: ‘rev’ when loading ‘easyRNASeq’ * DONE (easyRNASeq)
easyRNASeq.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> # get the example data and annotation files from GitHub
> 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(download.file(paste0("https://github.com/UPSCb/UPSCb/raw/",
+ "master/tutorial/easyRNASeq/",f),f))
+ }
+ }))
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/gAnnot.rda'
Content type 'application/octet-stream' length 796869 bytes (778 KB)
==================================================
downloaded 778 KB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz'
Content type 'application/octet-stream' length 5634837 bytes (5.4 MB)
==================================================
downloaded 5.4 MB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/Dmel-mRNA-exon-r5.52.gff3.gz'
Content type 'application/octet-stream' length 2218655 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACACTG.bam'
Content type 'application/octet-stream' length 2468525 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACTAGC.bam'
Content type 'application/octet-stream' length 1879955 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ATGGCT.bam'
Content type 'application/octet-stream' length 2415448 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/TTGCGA.bam'
Content type 'application/octet-stream' length 2643153 bytes (2.5 MB)
==================================================
downloaded 2.5 MB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACACTG.bam.bai'
Content type 'application/octet-stream' length 138024 bytes (134 KB)
==================================================
downloaded 134 KB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACTAGC.bam.bai'
Content type 'application/octet-stream' length 136128 bytes (132 KB)
==================================================
downloaded 132 KB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ATGGCT.bam.bai'
Content type 'application/octet-stream' length 137392 bytes (134 KB)
==================================================
downloaded 134 KB
trying URL 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/TTGCGA.bam.bai'
Content type 'application/octet-stream' length 140784 bytes (137 KB)
==================================================
downloaded 137 KB
>
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
No methods found in package 'IRanges' for request: 'rev' when loading '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 -- Mon Apr 15 23:51:05 2019
***********************************************
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
There were 11 warnings (use warnings() to see them)
>
> # cleanup
> file.remove(exFiles)
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
> proc.time()
user system elapsed
61.264 2.080 76.951
easyRNASeq.Rcheck/easyRNASeq-Ex.timings
| name | user | system | elapsed | |
| DESeq-methods | 0 | 0 | 0 | |
| GenomicRanges-methods | 0.500 | 0.013 | 0.519 | |
| IRanges-methods | 0.001 | 0.000 | 0.000 | |
| Rsamtools-methods | 0.260 | 0.054 | 3.433 | |
| ShortRead-methods | 0.000 | 0.000 | 0.001 | |
| easyRNASeq-AnnotParam-accessors | 0.037 | 0.019 | 0.838 | |
| easyRNASeq-AnnotParam-class | 0.001 | 0.000 | 0.002 | |
| easyRNASeq-AnnotParam | 0.032 | 0.010 | 0.522 | |
| easyRNASeq-BamFileList | 0.223 | 0.048 | 1.809 | |
| easyRNASeq-BamParam-accessors | 0.002 | 0.000 | 0.002 | |
| easyRNASeq-BamParam-class | 0.001 | 0.000 | 0.001 | |
| easyRNASeq-BamParam | 0.002 | 0.000 | 0.003 | |
| easyRNASeq-RnaSeqParam-accessors | 0.004 | 0.000 | 0.005 | |
| easyRNASeq-RnaSeqParam-class | 0.001 | 0.000 | 0.001 | |
| easyRNASeq-RnaSeqParam | 0.005 | 0.001 | 0.006 | |
| easyRNASeq-accessors | 0 | 0 | 0 | |
| easyRNASeq-annotation-methods | 0.000 | 0.001 | 0.000 | |
| easyRNASeq-class | 0.001 | 0.000 | 0.001 | |
| easyRNASeq-correction-methods | 0.000 | 0.001 | 0.001 | |
| easyRNASeq-coverage-methods | 0 | 0 | 0 | |
| easyRNASeq-easyRNASeq | 0 | 0 | 0 | |
| easyRNASeq-island-methods | 0.001 | 0.000 | 0.000 | |
| easyRNASeq-package | 70.568 | 1.738 | 75.573 | |
| easyRNASeq-simpleRNASeq | 96.306 | 2.055 | 103.014 | |
| easyRNASeq-summarization-methods | 0.001 | 0.000 | 0.000 | |
| easyRNASeq-synthetic-transcripts | 59.888 | 1.533 | 63.289 | |
| edgeR-methods | 0 | 0 | 0 | |
| genomeIntervals-methods | 1.593 | 0.172 | 2.863 | |
| parallel-methods | 0 | 0 | 0 | |