Sarah Sheppard
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cleanUpdTSeq |
| Branch: RELEASE_3_7 |
| Last Commit: 3fb69d7 |
| Last Changed Date: 2018-04-30 10:35:30 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:25:17 -0400 (Wed, 17 Oct 2018).
| Package 251/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cleanUpdTSeq 1.18.0 Sarah Sheppard
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cleanUpdTSeq |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cleanUpdTSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cleanUpdTSeq_1.18.0.tar.gz |
| StartedAt: 2018-10-15 23:15:56 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:20:03 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 247.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cleanUpdTSeq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cleanUpdTSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cleanUpdTSeq_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/cleanUpdTSeq.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 ‘cleanUpdTSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cleanUpdTSeq’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘BSgenome’ ‘BSgenome.Drerio.UCSC.danRer7’
‘GenomicRanges’ ‘seqinr’ ‘e1071’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘cleanUpdTSeq’ 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 ... NOTE
BED2GRangesSeq: no visible global function definition for ‘IRanges’
buildClassifier: no visible global function definition for ‘as.formula’
getDownstreamSequence: no visible global function definition for
‘IRanges’
getDownstreamSequence: no visible global function definition for
‘seqlengths’
getUpstreamSequence: no visible global function definition for
‘IRanges’
getUpstreamSequence: no visible global function definition for
‘seqlengths’
predictTestSet: no visible global function definition for ‘as.formula’
predictTestSet: no visible global function definition for ‘predict’
predictTestSet: no visible global function definition for ‘write.table’
Undefined global functions or variables:
IRanges as.formula predict seqlengths write.table
Consider adding
importFrom("stats", "as.formula", "predict")
importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictTestSet 26.04 0.108 26.222
data.NaiveBayes 22.90 0.172 23.102
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/cleanUpdTSeq.Rcheck/00check.log’
for details.
cleanUpdTSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL cleanUpdTSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘cleanUpdTSeq’ ... ** R ** data ** 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 (cleanUpdTSeq)
cleanUpdTSeq.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.
> require("cleanUpdTSeq") || stop("unable to load Package:cleanUpdTSeq")
Loading required package: cleanUpdTSeq
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 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: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: seqinr
Attaching package: 'seqinr'
The following object is masked from 'package:Biostrings':
translate
Loading required package: e1071
[1] TRUE
> BiocGenerics:::testPackage("cleanUpdTSeq")
RUNIT TEST PROTOCOL -- Mon Oct 15 23:20:00 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
cleanUpdTSeq RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
13.932 0.304 14.369
cleanUpdTSeq.Rcheck/cleanUpdTSeq-Ex.timings
| name | user | system | elapsed | |
| BED2GRangesSeq | 0.560 | 0.004 | 0.574 | |
| PASclassifier-class | 0.040 | 0.000 | 0.048 | |
| buildClassifier | 0.000 | 0.000 | 0.001 | |
| buildFeatureVector | 1.788 | 0.068 | 1.872 | |
| classifier | 0.036 | 0.000 | 0.037 | |
| cleanUpdTSeq-package | 0.000 | 0.000 | 0.003 | |
| data.NaiveBayes | 22.900 | 0.172 | 23.102 | |
| getDownstreamSequence | 0.112 | 0.000 | 0.113 | |
| getUpstreamSequence | 0.116 | 0.000 | 0.117 | |
| predictTestSet | 26.040 | 0.108 | 26.222 | |