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BioC 3.5: CHECK report for cleanUpdTSeq on tokay2

This page was generated on 2017-08-16 13:22:28 -0400 (Wed, 16 Aug 2017).

Package 225/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cleanUpdTSeq 1.14.0
Sarah Sheppard ; Jianhong Ou
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cleanUpdTSeq
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cleanUpdTSeq
Version: 1.14.0
Command: rm -rf cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && mkdir cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.14.0.tar.gz >cleanUpdTSeq.Rcheck\00install.out 2>&1 && cp cleanUpdTSeq.Rcheck\00install.out cleanUpdTSeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.14.0.tar.gz
StartedAt: 2017-08-15 22:43:56 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:51:35 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 459.1 seconds
RetCode: 0
Status:  OK  
CheckDir: cleanUpdTSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && mkdir cleanUpdTSeq.buildbin-libdir cleanUpdTSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cleanUpdTSeq.buildbin-libdir cleanUpdTSeq_1.14.0.tar.gz >cleanUpdTSeq.Rcheck\00install.out 2>&1 && cp cleanUpdTSeq.Rcheck\00install.out cleanUpdTSeq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cleanUpdTSeq.buildbin-libdir --install="check:cleanUpdTSeq-install.out" --force-multiarch --no-vignettes --timings cleanUpdTSeq_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cleanUpdTSeq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.14.0'
* 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 installed files from 'inst/doc' ... 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 27.77   2.63   30.39
predictTestSet  28.34   0.27   28.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
data.NaiveBayes 18.77   0.16   18.92
predictTestSet  18.42   0.08   18.50
* 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-3.5-bioc/meat/cleanUpdTSeq.Rcheck/00check.log'
for details.


cleanUpdTSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'cleanUpdTSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cleanUpdTSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cleanUpdTSeq' as cleanUpdTSeq_1.14.0.zip
* DONE (cleanUpdTSeq)

cleanUpdTSeq.Rcheck/examples_i386/cleanUpdTSeq-Ex.timings:

nameusersystemelapsed
BED2GRangesSeq0.080.000.08
PASclassifier-class0.050.000.05
buildClassifier000
buildFeatureVector3.750.073.85
classifier0.060.000.06
cleanUpdTSeq-package000
data.NaiveBayes27.77 2.6330.39
getDownstreamSequence0.140.000.14
getUpstreamSequence0.160.000.16
predictTestSet28.34 0.2728.79

cleanUpdTSeq.Rcheck/examples_x64/cleanUpdTSeq-Ex.timings:

nameusersystemelapsed
BED2GRangesSeq0.060.010.08
PASclassifier-class0.010.030.05
buildClassifier000
buildFeatureVector3.710.003.70
classifier0.040.000.05
cleanUpdTSeq-package000
data.NaiveBayes18.77 0.1618.92
getDownstreamSequence0.140.000.14
getUpstreamSequence0.170.000.17
predictTestSet18.42 0.0818.50