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BioC 3.6: CHECK report for exomeCopy on malbec1

This page was generated on 2017-08-16 13:19:51 -0400 (Wed, 16 Aug 2017).

Package 426/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomeCopy 1.23.2
Michael Love
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/exomeCopy
Last Changed Rev: 129166 / Revision: 131943
Last Changed Date: 2017-04-25 10:21:23 -0400 (Tue, 25 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: exomeCopy
Version: 1.23.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings exomeCopy_1.23.2.tar.gz
StartedAt: 2017-08-15 23:00:54 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:02:30 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 95.7 seconds
RetCode: 0
Status:  OK 
CheckDir: exomeCopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings exomeCopy_1.23.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/exomeCopy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomeCopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomeCopy’ version ‘1.23.2’
* 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 ‘exomeCopy’ 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 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
emFn : <anonymous>: no visible global function definition for ‘dnbinom’
exomeCopy: no visible global function definition for ‘lm’
exomeCopy: no visible global function definition for ‘optim’
exomeCopy: no visible global function definition for ‘new’
exomeCopy: no visible global function definition for ‘Rle’
getGCcontent: no visible global function definition for
  ‘letterFrequency’
plot.ExomeCopy: no visible global function definition for ‘segments’
plot.ExomeCopy: no visible global function definition for ‘legend’
plotCompiledCNV: no visible global function definition for ‘axis’
plotCompiledCNV: no visible global function definition for ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
  ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  Rle axis dnbinom legend letterFrequency lm new optim segments
Consider adding
  importFrom("graphics", "axis", "legend", "segments")
  importFrom("methods", "new")
  importFrom("stats", "dnbinom", "lm", "optim")
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
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/exomeCopy.Rcheck/00check.log’
for details.


exomeCopy.Rcheck/00install.out:

* installing *source* package ‘exomeCopy’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c exomeCopy.c -o exomeCopy.o
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o exomeCopy.so exomeCopy.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/exomeCopy.Rcheck/exomeCopy/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 (exomeCopy)

exomeCopy.Rcheck/exomeCopy-Ex.timings:

nameusersystemelapsed
ExomeCopy-class0.0000.0000.001
compileCopyCountSegments3.7920.0483.841
copyCountSegments3.4120.0003.417
countBamInGRanges0.620.000.62
exomeCopy3.4640.0003.467
generateBackground0.1200.0000.121
getGCcontent0.0160.0000.016
negLogLike0.0080.0000.008
plot.exomeCopyObject3.320.003.32
plotCompiledCNV3.1440.0003.147
subdivideGRanges0.1080.0000.105