Charles Joly Beauparlant
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/metagene |
| Branch: RELEASE_3_9 |
| Last Commit: 89b13a0 |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:53:40 -0400 (Wed, 16 Oct 2019).
| Package 961/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagene 2.16.0 Charles Joly Beauparlant
| 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: metagene |
| Version: 2.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagene_2.16.0.tar.gz |
| StartedAt: 2019-10-16 04:26:08 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:35:32 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 563.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metagene.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagene_2.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/metagene.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 ‘metagene/DESCRIPTION’ ... OK
* this is package ‘metagene’ version ‘2.16.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘metagene’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
extdata 5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘similaRpeak’
A package should be listed in only one of these fields.
* 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 ... NOTE
avoid_gaps_update: no visible binding for global variable 'value'
avoid_gaps_update: no visible binding for global variable 'bam'
avoid_gaps_update: no visible binding for global variable 'tab'
avoid_gaps_update: no visible binding for global variable 'nuc'
permutation_test: no visible global function definition for '.'
permutation_test: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'bin'
plot_metagene: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'qinf'
plot_metagene: no visible binding for global variable 'qsup'
plot_metagene: no visible binding for global variable 'group'
plot_metagene: no visible binding for global variable 'nuc'
plot_metagene: no visible binding for global variable 'design'
plot_metagene: no visible binding for global variable 'nuctot'
Undefined global functions or variables:
. bam bin design group nuc nuctot qinf qsup tab value
* 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 R/sysdata.rda ... 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
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/metagene.Rcheck/00check.log’
for details.
metagene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metagene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘metagene’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (metagene)
metagene.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.
> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene")
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
[1] TRUE
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE
RUNIT TEST PROTOCOL -- Wed Oct 16 04:35:24 2019
***********************************************
Number of test functions: 219
Number of errors: 0
Number of failures: 0
1 Test Suite :
metagene RUnit Tests - 219 test functions, 0 errors, 0 failures
Number of test functions: 219
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
157.505 32.182 154.255
metagene.Rcheck/metagene-Ex.timings
| name | user | system | elapsed | |
| Bam_Handler | 0.168 | 0.008 | 0.179 | |
| avoid_gaps_update | 0.001 | 0.002 | 0.002 | |
| bed_file_filter | 0.000 | 0.001 | 0.000 | |
| exon_by_gene_with_observed_transcripts | 0 | 0 | 0 | |
| get_demo_bam_files | 0.004 | 0.001 | 0.005 | |
| get_demo_design | 0.003 | 0.001 | 0.005 | |
| get_demo_metagene | 3.097 | 0.414 | 3.523 | |
| get_demo_regions | 0.002 | 0.000 | 0.002 | |
| get_promoters_txdb | 0 | 0 | 0 | |
| metagene | 0.407 | 0.012 | 0.421 | |
| permutation_test | 0 | 0 | 0 | |
| plot_metagene | 1.967 | 0.896 | 1.578 | |
| promoters_hg18 | 0.018 | 0.017 | 0.007 | |
| promoters_hg19 | 0.011 | 0.012 | 0.006 | |
| promoters_mm10 | 0.014 | 0.014 | 0.005 | |
| promoters_mm9 | 0.015 | 0.017 | 0.006 | |
| write_bed_file_filter_result | 0.002 | 0.003 | 0.001 | |