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BioC 3.5: CHECK report for contiBAIT on oaxaca

This page was generated on 2017-03-04 16:51:42 -0500 (Sat, 04 Mar 2017).

Package 260/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.3.0
Kieran O'Neill
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/contiBAIT
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: contiBAIT
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings contiBAIT_1.3.0.tar.gz
StartedAt: 2017-03-04 01:08:59 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 01:13:52 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 293.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: contiBAIT.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings contiBAIT_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/contiBAIT.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘contiBAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘contiBAIT’ version ‘1.3.0’
* 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 ‘contiBAIT’ 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 loading without being on the library search path ... 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
clusterContigs.func : runOnce: no visible global function definition
  for ‘runif’
locateMisorients.func: no visible global function definition for
  ‘unstrand’
makeBoxPlot.func: no visible global function definition for ‘boxplot’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
mergeFlankedLGs.func: no visible binding for global variable ‘head’
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for ‘head’
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for ‘tail’
plotContigOrder.func: no visible global function definition for ‘lm’
plotLGDistances.func: no visible global function definition for
  ‘legend’
plotWCdistribution.func : <anonymous>: no visible global function
  definition for ‘hist’
plotWCdistribution.func: no visible global function definition for
  ‘rbinom’
plotWCdistribution.func: no visible global function definition for
  ‘boxplot’
plotWCdistribution.func: no visible global function definition for
  ‘lines’
plotWCdistribution.func: no visible global function definition for
  ‘text’
clusterContigs,StrandStateMatrix : runOnce: no visible global function
  definition for ‘runif’
locateMisorients,GRanges: no visible global function definition for
  ‘unstrand’
makeBoxPlot,ChrTable-LinkageGroupList: no visible global function
  definition for ‘boxplot’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix: no visible binding
  for global variable ‘head’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for ‘head’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for ‘tail’
plotContigOrder,ContigOrdering: no visible global function definition
  for ‘lm’
plotLGDistances,LinkageGroupList-StrandStateMatrix: no visible global
  function definition for ‘legend’
plotWCdistribution,StrandFreqMatrix : <anonymous>: no visible global
  function definition for ‘hist’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘rbinom’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘boxplot’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘lines’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘text’
show,ContigOrdering: no visible global function definition for ‘head’
show,ContigOrdering: no visible global function definition for ‘tail’
show,LibraryGroupList: no visible global function definition for ‘head’
show,LibraryGroupList: no visible global function definition for ‘tail’
show,LinkageGroupList: no visible global function definition for ‘head’
show,LinkageGroupList: no visible global function definition for ‘tail’
show,StrandStateList: no visible global function definition for ‘head’
show,StrandStateList: no visible global function definition for ‘tail’
Undefined global functions or variables:
  boxplot head hist legend lines lm queryHits rbinom runif subjectHits
  tail text unstrand
Consider adding
  importFrom("graphics", "boxplot", "hist", "legend", "lines", "text")
  importFrom("stats", "lm", "rbinom", "runif")
  importFrom("utils", "head", "tail")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'switch' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
           user system elapsed
contiBAIT 9.919  0.185  10.107
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.


contiBAIT.Rcheck/00install.out:

* installing *source* package ‘contiBAIT’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c computeSim.cpp -o computeSim.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o contiBAIT.so computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/contiBAIT.Rcheck/contiBAIT/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (contiBAIT)

contiBAIT.Rcheck/contiBAIT-Ex.timings:

nameusersystemelapsed
BAIT0.0010.0000.001
ContigOrdering0.0020.0000.003
LibraryGroupList0.0130.0010.013
LinkageGroupList0.0010.0000.001
OrientationFrame0.010.000.01
StrandFreqMatrix0.0320.0050.037
StrandReadMatrix0.4640.0030.468
StrandStateMatrix0.0030.0000.003
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method1.5600.0501.611
clusterContigs-StrandStateMatrix-method1.8840.0081.893
contiBAIT 9.919 0.18510.107
findSimilarLibraries2.9240.0292.956
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method3.3040.0393.345
makeBoxPlot0.0340.0020.038
makeChrTable1.1740.0111.185
orderAllLinkageGroups0.5910.0190.610
plotContigOrder0.8810.0060.888
plotLGDistances-LinkageGroupList-StrandStateMatrix-method1.1310.0081.142
plotWCdistribution-StrandFreqMatrix-method0.1000.0030.104
preprocessStrandTable-StrandFreqMatrix-method0.3610.0020.364
reorientAndMergeLGs1.7270.0071.734
strandSeqFreqTable4.3950.1744.573
thoroughBed0.0340.0020.035
writeBed000