| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:56:40 -0400 (Tue, 16 Apr 2019).
| Package 475/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ensemblVEP 1.24.2 Bioconductor Package Maintainer
| 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: ensemblVEP |
| Version: 1.24.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ensemblVEP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ensemblVEP_1.24.2.tar.gz |
| StartedAt: 2019-04-15 23:46:18 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:51:56 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 338.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ensemblVEP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ensemblVEP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ensemblVEP_1.24.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ensemblVEP.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 ‘ensemblVEP/DESCRIPTION’ ... OK
* this is package ‘ensemblVEP’ version ‘1.24.2’
* 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:
.BBSoptions
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 ‘ensemblVEP’ 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 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
parseCSQToGRanges 3.243 0.322 19.079
ensemblVEP 2.905 0.322 19.256
* 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/ensemblVEP.Rcheck/00check.log’
for details.
ensemblVEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ensemblVEP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ensemblVEP’ ... ** 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 (ensemblVEP)
ensemblVEP.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.
> BiocGenerics:::testPackage("ensemblVEP")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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 objects are masked from 'package:base':
aperm, apply
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Attaching package: 'ensemblVEP'
The following object is masked from 'package:Biobase':
cache
-------------------- EXCEPTION --------------------
MSG: ERROR: File "ImNotAFile" does not exist
STACK Bio::EnsEMBL::VEP::Parser::file /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:232
STACK Bio::EnsEMBL::VEP::Parser::new /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:125
STACK Bio::EnsEMBL::VEP::Runner::get_Parser /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:789
STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:815
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:131
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/ensembl-vep/vep:218
Date (localtime) = Mon Apr 15 23:51:51 2019
Ensembl API version = 96
---------------------------------------------------
RUNIT TEST PROTOCOL -- Mon Apr 15 23:51:51 2019
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
ensemblVEP RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.898 1.269 41.635
ensemblVEP.Rcheck/ensemblVEP-Ex.timings
| name | user | system | elapsed | |
| VEPFlags-class | 0.022 | 0.017 | 0.039 | |
| VEPParam-class | 0.056 | 0.013 | 0.070 | |
| ensemblVEP | 2.905 | 0.322 | 19.256 | |
| oldRuntimeOptions | 0.001 | 0.000 | 0.000 | |
| parseCSQToGRanges | 3.243 | 0.322 | 19.079 | |
| runtimeOptions | 0.001 | 0.001 | 0.001 | |