Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:05:41 -0400 (Fri, 24 Sep 2021).

CHECK results for cleanUpdTSeq on nebbiolo1

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cleanUpdTSeq.git to
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raw results

Package 318/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleanUpdTSeq 1.30.0  (landing page)
Jianhong Ou ; Lihua Julie Zhu
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/cleanUpdTSeq
git_branch: RELEASE_3_13
git_last_commit: 45e4e8b
git_last_commit_date: 2021-05-19 11:59:31 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cleanUpdTSeq
Version: 1.30.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cleanUpdTSeq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cleanUpdTSeq_1.30.0.tar.gz
StartedAt: 2021-09-23 09:14:21 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 09:18:44 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 262.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cleanUpdTSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cleanUpdTSeq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cleanUpdTSeq_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cleanUpdTSeq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.30.0’
* package encoding: UTF-8
* 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 ‘cleanUpdTSeq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    extdata   1.2Mb
* 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 ... NOTE
  Error loading dataset 'classifier':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed
  
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
data.NaiveBayes 5.25  1.779   7.030
predictTestSet  6.06  0.812   6.872
* 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-3.13-bioc/meat/cleanUpdTSeq.Rcheck/00check.log’
for details.



Installation output

cleanUpdTSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cleanUpdTSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cleanUpdTSeq’ ...
** 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 (cleanUpdTSeq)

Tests output

cleanUpdTSeq.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: BSgenome.Drerio.UCSC.danRer7
Loading required package: BSgenome
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, 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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

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
[1] TRUE
> BiocGenerics:::testPackage("cleanUpdTSeq")
genome of classifier is different from testSet.NaiveBayes.


RUNIT TEST PROTOCOL -- Thu Sep 23 09:18:41 2021 
*********************************************** 
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 
 12.481   0.846  13.314 

Example timings

cleanUpdTSeq.Rcheck/cleanUpdTSeq-Ex.timings

nameusersystemelapsed
BED6WithSeq2GRangesSeq0.1260.0120.138
PASclassifier-class0.0090.0120.022
buildClassifier000
buildFeatureVector1.5710.0791.649
classifier0.0220.0030.026
data.NaiveBayes5.2501.7797.030
getContextSequences0.4010.0200.420
predictTestSet6.0600.8126.872