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CHECK report for cleanUpdTSeq on tokay2

This page was generated on 2018-10-17 08:37:25 -0400 (Wed, 17 Oct 2018).

Package 251/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleanUpdTSeq 1.18.0
Sarah Sheppard ; Jianhong Ou
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)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cleanUpdTSeq
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cleanUpdTSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cleanUpdTSeq_1.18.0.tar.gz
StartedAt: 2018-10-17 01:08:51 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:16:30 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 458.5 seconds
RetCode: 0
Status:  OK  
CheckDir: cleanUpdTSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cleanUpdTSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cleanUpdTSeq_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cleanUpdTSeq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
data.NaiveBayes 27.14   3.87   31.13
predictTestSet  26.20   0.68   26.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
predictTestSet  36.11   0.25   36.36
data.NaiveBayes 30.17   0.44   30.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.



Installation output

cleanUpdTSeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cleanUpdTSeq_1.18.0.tar.gz && rm -rf cleanUpdTSeq.buildbin-libdir && mkdir cleanUpdTSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cleanUpdTSeq_1.18.0.zip && rm cleanUpdTSeq_1.18.0.tar.gz cleanUpdTSeq_1.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3930k  100 3930k    0     0  38.4M      0 --:--:-- --:--:-- --:--:-- 41.2M

install for i386

* installing *source* package 'cleanUpdTSeq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cleanUpdTSeq'
    finding HTML links ... done
    BED2GRangesSeq                          html  
    PASclassifier-class                     html  
    buildClassifier                         html  
    buildFeatureVector                      html  
    classifier                              html  
    cleanUpdTSeq-package                    html  
    data.NaiveBayes                         html  
    featureVector-class                     html  
    getDownstreamSequence                   html  
    getUpstreamSequence                     html  
    modelInfo-class                         html  
    naiveBayes                              html  
    predictTestSet                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cleanUpdTSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cleanUpdTSeq' as cleanUpdTSeq_1.18.0.zip
* DONE (cleanUpdTSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cleanUpdTSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

cleanUpdTSeq.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

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
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 -- Wed Oct 17 01:16:04 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 
  19.78    0.75   20.92 

cleanUpdTSeq.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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: 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

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
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 -- Wed Oct 17 01:16:23 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 
  17.92    0.50   18.40 

Example timings

cleanUpdTSeq.Rcheck/examples_i386/cleanUpdTSeq-Ex.timings

nameusersystemelapsed
BED2GRangesSeq0.030.010.04
PASclassifier-class0.050.000.05
buildClassifier000
buildFeatureVector2.340.252.60
classifier0.050.000.04
cleanUpdTSeq-package000
data.NaiveBayes27.14 3.8731.13
getDownstreamSequence0.090.000.09
getUpstreamSequence0.110.000.11
predictTestSet26.20 0.6826.97

cleanUpdTSeq.Rcheck/examples_x64/cleanUpdTSeq-Ex.timings

nameusersystemelapsed
BED2GRangesSeq0.070.020.09
PASclassifier-class0.080.000.08
buildClassifier000
buildFeatureVector3.680.093.77
classifier0.040.000.05
cleanUpdTSeq-package0.020.000.01
data.NaiveBayes30.17 0.4430.61
getDownstreamSequence0.20.00.2
getUpstreamSequence0.220.000.22
predictTestSet36.11 0.2536.36