Back to the "Multiple platform build/check report" A  B  C  D  E  F  G [H] I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.13: CHECK report for HiTC on zin1

This page was generated on 2014-04-05 09:48:17 -0700 (Sat, 05 Apr 2014).

Package 346/750HostnameOS / ArchBUILDCHECKBUILD BIN
HiTC 1.6.0
Nicolas Servant
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/HiTC
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: HiTC
Version: 1.6.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.6.0.tar.gz
StartedAt: 2014-04-05 01:51:11 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:55:33 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:  OK 
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/HiTC.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.6.0’
* 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 ‘HiTC’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘rtracklayer’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ‘:::’ call: ‘Matrix:::is0’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘HiTC.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [69s/69s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              11.944  0.044  12.025
HTCexp-class       9.560  0.060   9.647
CQC                8.953  0.052   9.020
getExpectedCounts  7.868  0.148   7.849
binningC           6.477  0.008   6.495
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/HiTC.Rcheck/00check.log’
for details.

HiTC.Rcheck/00install.out:

* installing *source* package ‘HiTC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘HiTC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HiTC)

HiTC.Rcheck/HiTC-Ex.timings:

nameusersystemelapsed
CQC8.9530.0529.020
HTCexp-class9.5600.0609.647
HTClist-class3.3960.4163.569
Nora_5C0.2440.0160.259
binningC6.4770.0086.495
discretize0.0120.0000.009
export.my5C0.0040.0000.002
exportC0.0040.0040.008
extractRegion0.4920.0040.496
getExpectedCounts7.8680.1487.849
import.my5C0.5480.0040.552
importC0.0040.0000.001
intervalsDist4.0850.0084.215
mapC11.944 0.04412.025
pca.hic2.0040.3922.105
removeIntervals0.3570.0040.363
setIntervalScale2.5800.0042.591