BioC 2.14: CHECK report for HiTC on zin2

Package: HiTC

Version: 1.8.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.8.1.tar.gz

StartedAt: 2014-10-08 00:25:29 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:30:09 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 280.0 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/HiTC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.8.1’
* 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 ... [22s/22s] 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
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [51s/50s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
mapC     8.904  0.048   9.000
binningC 6.624  0.040   6.692
CQC      6.277  0.036   6.322
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/HiTC.Rcheck/00check.log’
for details.

* installing *source* package ‘HiTC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘isSymmetric’ from package ‘base’ in package ‘HiTC’
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)

name	user	system	elapsed
CQC	6.277	0.036	6.322
HTCexp-class	4.412	0.060	4.479
HTClist-class	3.316	0.388	3.417
Nora_5C	0.244	0.012	0.257
binningC	6.624	0.040	6.692
discretize	0.004	0.000	0.001
export.my5C	0.000	0.000	0.001
exportC	0	0	0
extractRegion	0.488	0.004	0.494
getAnnotatedRestrictionSites	0.004	0.000	0.001
getExpectedCounts	2.637	0.144	2.610
import.my5C	0.548	0.008	0.558
importC	0.000	0.000	0.001
intervalsDist	0.488	0.012	0.502
mapC	8.904	0.048	9.000
normICE	0	0	0
normLGF	0.004	0.000	0.001
pca.hic	1.888	0.408	1.967
removeIntervals	0.372	0.008	0.379
setGenomicFeatures	0.004	0.000	0.001
setIntervalScale	2.460	0.008	2.472