Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-18 11:06:58 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cleanUpdTSeq on riesling1


To the developers/maintainers of the cleanUpdTSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cleanUpdTSeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 322/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleanUpdTSeq 1.33.0  (landing page)
Jianhong Ou ; Lihua Julie Zhu
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/cleanUpdTSeq
git_branch: master
git_last_commit: ddeaa93
git_last_commit_date: 2021-10-26 12:08:46 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BSgenome' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cleanUpdTSeq
Version: 1.33.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cleanUpdTSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cleanUpdTSeq_1.33.0.tar.gz
StartedAt: 2022-01-17 18:35:09 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 18:39:03 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 234.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cleanUpdTSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cleanUpdTSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cleanUpdTSeq_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cleanUpdTSeq.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cleanUpdTSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cleanUpdTSeq' version '1.33.0'
* 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 whether package 'cleanUpdTSeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    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
predictTestSet  6.40   2.02    8.42
data.NaiveBayes 3.68   1.45    5.14
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.



Installation output

cleanUpdTSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cleanUpdTSeq
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'cleanUpdTSeq'
    finding HTML links ... done
    BED6WithSeq2GRangesSeq                  html  
    PASclassifier-class                     html  
    buildClassifier                         html  
    buildFeatureVector                      html  
    classifier                              html  
    cleanUpdTSeq                            html  
    data.NaiveBayes                         html  
    featureVector-class                     html  
    getContextSequences                     html  
    modelInfo-class                         html  
    naiveBayes-class                        html  
    predictTestSet                          html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Gviz' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SpatialDecon' is missing or broken
 done

Tests output

cleanUpdTSeq.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'BiocGenerics'

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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 -- Mon Jan 17 18:38:51 2022 
*********************************************** 
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 
  12.06    1.15   13.20 

Example timings

cleanUpdTSeq.Rcheck/cleanUpdTSeq-Ex.timings

nameusersystemelapsed
BED6WithSeq2GRangesSeq0.080.030.11
PASclassifier-class0.000.030.03
buildClassifier000
buildFeatureVector1.730.051.78
classifier0.020.000.01
data.NaiveBayes3.681.455.14
getContextSequences0.430.000.43
predictTestSet6.402.028.42