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BioC 2.13: CHECK report for HiTC on moscato1

This page was generated on 2014-04-05 09:50:48 -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: rm -rf HiTC.buildbin-libdir && mkdir HiTC.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.6.0.tar.gz >HiTC-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.6.0.tar.gz && mv HiTC.buildbin-libdir/* HiTC.Rcheck/ && rmdir HiTC.buildbin-libdir
StartedAt: 2014-04-05 04:34:08 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:42:01 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 473.3 seconds
RetCode: 0
Status:  OK  
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/HiTC.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'HiTC' can be installed ... 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
* 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 ... 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 ...
** running examples for arch 'i386' ... [83s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mapC              14.61   0.25   15.04
HTCexp-class      13.46   0.31   13.78
CQC               10.89   0.05   10.94
getExpectedCounts  8.61   0.11    8.72
binningC           7.52   0.00    7.52
intervalsDist      5.60   0.00    5.60
** running examples for arch 'x64' ... [94s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mapC              17.22   0.29   17.60
HTCexp-class      13.14   0.11   13.25
CQC               12.42   0.14   12.56
getExpectedCounts 11.88   0.08   11.98
binningC           8.87   0.00    8.88
intervalsDist      5.95   0.00    5.94
* 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
  'D:/biocbld/bbs-2.13-bioc/meat/HiTC.Rcheck/00check.log'
for details.

HiTC.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'HiTC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiTC' as HiTC_1.6.0.zip
* DONE (HiTC)

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

nameusersystemelapsed
CQC10.89 0.0510.94
HTCexp-class13.46 0.3113.78
HTClist-class4.030.024.04
Nora_5C0.210.000.22
binningC7.520.007.52
discretize0.000.010.01
export.my5C000
exportC000
extractRegion0.50.00.5
getExpectedCounts8.610.118.72
import.my5C0.50.00.5
importC000
intervalsDist5.60.05.6
mapC14.61 0.2515.04
pca.hic2.090.022.10
removeIntervals0.380.030.41
setIntervalScale2.620.022.63

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

nameusersystemelapsed
CQC12.42 0.1412.56
HTCexp-class13.14 0.1113.25
HTClist-class4.760.024.79
Nora_5C0.270.010.28
binningC8.870.008.88
discretize0.020.000.01
export.my5C000
exportC0.020.000.01
extractRegion0.850.000.84
getExpectedCounts11.88 0.0811.98
import.my5C0.630.000.63
importC000
intervalsDist5.950.005.94
mapC17.22 0.2917.60
pca.hic2.310.032.36
removeIntervals0.350.020.36
setIntervalScale2.990.003.00