Nicolas Delhomme
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/easyRNASeq |
| Branch: RELEASE_3_9 |
| Last Commit: df675a9 |
| Last Changed Date: 2019-05-02 11:53:34 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:49:44 -0400 (Wed, 16 Oct 2019).
| Package 476/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| easyRNASeq 2.20.0 Nicolas Delhomme
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: easyRNASeq |
| Version: 2.20.0 |
| 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_2.20.0.tar.gz |
| StartedAt: 2019-10-16 02:27:47 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:42:57 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 909.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: easyRNASeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_2.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/easyRNASeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.20.0’
* 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 126.546 4.079 137.180
easyRNASeq-package 100.713 4.040 107.497
easyRNASeq-synthetic-transcripts 74.021 1.929 77.296
easyRNASeq-BamFileList 16.928 0.550 19.223
Rsamtools-methods 13.380 0.542 15.787
BiocFileCache-methods 11.538 0.513 20.257
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘easyRNASeq’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (easyRNASeq)
easyRNASeq.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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
> library(easyRNASeq)
> tutorialData()
[1] "/Users/biocbuild/Library/Caches/easyRNASeq"
>
> # set the env.var
> #TUTORIAL.DATA <- get("TUTORIAL.DATA",envir=as.environment("package:easyRNASeq"))
>
> # 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, 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, 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 -- Wed Oct 16 02:42:46 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 21 warnings (use warnings() to see them)
>
> # cleanup
> # removebfc(easyRNASeq:::.get_cache(),ask=FALSE)
>
> proc.time()
user system elapsed
120.592 5.557 142.886
easyRNASeq.Rcheck/easyRNASeq-Ex.timings
| name | user | system | elapsed | |
| BiocFileCache-methods | 11.538 | 0.513 | 20.257 | |
| DESeq-methods | 0.001 | 0.000 | 0.001 | |
| GenomicRanges-methods | 0.683 | 0.035 | 0.719 | |
| IRanges-methods | 0.001 | 0.000 | 0.001 | |
| Rsamtools-methods | 13.380 | 0.542 | 15.787 | |
| ShortRead-methods | 0.001 | 0.001 | 0.003 | |
| easyRNASeq-AnnotParam-accessors | 0.858 | 0.037 | 0.981 | |
| easyRNASeq-AnnotParam-class | 0.002 | 0.000 | 0.002 | |
| easyRNASeq-AnnotParam | 0.846 | 0.025 | 0.954 | |
| easyRNASeq-BamFileList | 16.928 | 0.550 | 19.223 | |
| easyRNASeq-BamParam-accessors | 0.001 | 0.001 | 0.002 | |
| easyRNASeq-BamParam-class | 0.001 | 0.000 | 0.002 | |
| easyRNASeq-BamParam | 0.004 | 0.001 | 0.005 | |
| easyRNASeq-RnaSeqParam-accessors | 0.003 | 0.001 | 0.003 | |
| easyRNASeq-RnaSeqParam-class | 0.001 | 0.000 | 0.001 | |
| easyRNASeq-RnaSeqParam | 0.006 | 0.001 | 0.007 | |
| easyRNASeq-accessors | 0.000 | 0.001 | 0.001 | |
| easyRNASeq-annotation-methods | 0.001 | 0.001 | 0.001 | |
| easyRNASeq-class | 0.002 | 0.001 | 0.002 | |
| easyRNASeq-correction-methods | 0.001 | 0.000 | 0.002 | |
| easyRNASeq-coverage-methods | 0.001 | 0.001 | 0.002 | |
| easyRNASeq-easyRNASeq | 0.001 | 0.001 | 0.002 | |
| easyRNASeq-island-methods | 0.001 | 0.001 | 0.001 | |
| easyRNASeq-package | 100.713 | 4.040 | 107.497 | |
| easyRNASeq-simpleRNASeq | 126.546 | 4.079 | 137.180 | |
| easyRNASeq-summarization-methods | 0.001 | 0.001 | 0.001 | |
| easyRNASeq-synthetic-transcripts | 74.021 | 1.929 | 77.296 | |
| edgeR-methods | 0.001 | 0.001 | 0.001 | |
| genomeIntervals-methods | 2.929 | 0.161 | 3.848 | |
| parallel-methods | 0.001 | 0.000 | 0.001 | |