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BioC 3.4: CHECK report for TitanCNA on malbec1

This page was generated on 2017-04-15 16:12:03 -0400 (Sat, 15 Apr 2017).

Package 1238/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.12.0
Gavin Ha , Sohrab P Shah
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/TitanCNA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TitanCNA
Version: 1.12.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TitanCNA_1.12.0.tar.gz
StartedAt: 2017-04-15 01:38:51 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:41:37 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 166.2 seconds
RetCode: 0
Status:  OK 
CheckDir: TitanCNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TitanCNA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TitanCNA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TitanCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TitanCNA’ version ‘1.12.0’
* 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 ‘TitanCNA’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   4.9Mb
* 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
correctReadDepth: no visible global function definition for ‘queryHits’
correctReadcount: no visible global function definition for ‘loess’
correctReadcount: no visible global function definition for ‘predict’
correctReadcount: no visible global function definition for ‘approxfun’
correctReadcount: no visible global function definition for ‘lowess’
extractAlleleReadCounts: no visible global function definition for
  ‘xtabs’
extractAlleleReadCounts: no visible global function definition for
  ‘write.table’
getPositionOverlap: no visible global function definition for ‘as’
getPositionOverlap: no visible global function definition for
  ‘queryHits’
getPositionOverlap: no visible global function definition for
  ‘subjectHits’
getSubcloneProfiles: no visible global function definition for
  ‘read.delim’
loadAlleleCounts: no visible global function definition for
  ‘read.delim’
outlierObslik: no visible global function definition for ‘dunif’
outputModelParameters: no visible global function definition for
  ‘write.table’
outputTitanResults: no visible global function definition for
  ‘write.table’
plotAllelicCN: no visible global function definition for ‘par’
plotAllelicCN: no visible global function definition for ‘plot’
plotAllelicCN: no visible global function definition for ‘lines’
plotAllelicRatio: no visible global function definition for ‘par’
plotAllelicRatio: no visible global function definition for ‘plot’
plotAllelicRatio: no visible global function definition for ‘lines’
plotCNlogRByChr: no visible global function definition for ‘par’
plotCNlogRByChr: no visible global function definition for ‘plot’
plotCNlogRByChr: no visible global function definition for ‘lines’
plotCNlogRByChr : <anonymous>: no visible global function definition
  for ‘lines’
plotChrLines: no visible global function definition for ‘lines’
plotChrLines: no visible global function definition for ‘axis’
plotClonalFrequency: no visible global function definition for ‘par’
plotClonalFrequency: no visible global function definition for ‘plot’
plotClonalFrequency: no visible global function definition for ‘lines’
plotClonalFrequency: no visible global function definition for ‘mtext’
plotGeneAnnotation: no visible global function definition for ‘abline’
plotGeneAnnotation: no visible global function definition for ‘mtext’
plotSegmentMedians: no visible global function definition for ‘par’
plotSegmentMedians: no visible global function definition for ‘plot’
plotSegmentMedians : <anonymous>: no visible global function definition
  for ‘lines’
plotSegmentMedians: no visible global function definition for ‘lines’
plotSubcloneProfiles: no visible global function definition for ‘par’
plotSubcloneProfiles: no visible global function definition for ‘plot’
plotSubcloneProfiles: no visible global function definition for ‘axis’
plotSubcloneProfiles: no visible global function definition for
  ‘points’
plotSubcloneProfiles: no visible global function definition for ‘mtext’
plotSubcloneProfiles: no visible global function definition for ‘lines’
printSDbw: no visible global function definition for ‘write.table’
removeEmptyClusters: no visible global function definition for ‘tail’
updateParameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline approxfun as axis dunif lines loess lowess mtext par plot
  points predict queryHits read.delim subjectHits tail uniroot
  write.table xtabs
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points")
  importFrom("methods", "as")
  importFrom("stats", "approxfun", "dunif", "loess", "lowess", "predict",
             "uniroot", "xtabs")
  importFrom("utils", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
TitanCNA-package   19.148  0.036  19.194
runEMclonalCN      15.688  0.032  15.730
getPositionOverlap  8.648  0.000   8.653
filterData          8.304  0.004   8.313
correctReadDepth    7.868  0.004   7.874
* 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-3.4-bioc/meat/TitanCNA.Rcheck/00check.log’
for details.


TitanCNA.Rcheck/00install.out:

* installing *source* package ‘TitanCNA’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c getPositionOverlapC.c -o getPositionOverlapC.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o TitanCNA.so fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/TitanCNA.Rcheck/TitanCNA/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 (TitanCNA)

TitanCNA.Rcheck/TitanCNA-Ex.timings:

nameusersystemelapsed
TitanCNA-output1.5320.0521.584
TitanCNA-package19.148 0.03619.194
TitanCNA-plotting1.1440.0161.160
computeSDbwIndex0.7720.0000.770
correctReadDepth7.8680.0047.874
extractAlleleReadCounts000
filterData8.3040.0048.313
getPositionOverlap8.6480.0008.653
loadAlleleCounts0.1240.0000.125
loadDefaultParameters000
removeEmptyClusters0.8400.0000.837
runEMclonalCN15.688 0.03215.730
viterbiClonalCN0.4840.0040.485
wigToRangedData0.3080.0000.309