BioC 2.14: CHECK report for HiTC on morelia

Package: HiTC

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HiTC_1.8.1.tar.gz

StartedAt: 2014-10-07 23:28:30 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:33:56 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 325.1 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HiTC_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/HiTC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [25s/25s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/58s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mapC         10.094  0.273  10.408
binningC      6.686  0.165   6.860
CQC           6.729  0.120   6.857
HTCexp-class  4.887  0.181   5.075
* 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
  ‘/Users/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	6.729	0.120	6.857
HTCexp-class	4.887	0.181	5.075
HTClist-class	4.209	0.748	4.540
Nora_5C	0.312	0.006	0.319
binningC	6.686	0.165	6.860
discretize	0.000	0.000	0.001
export.my5C	0.001	0.000	0.001
exportC	0.001	0.000	0.001
extractRegion	0.664	0.012	0.677
getAnnotatedRestrictionSites	0.001	0.000	0.001
getExpectedCounts	3.094	0.371	3.161
import.my5C	0.617	0.016	0.634
importC	0.001	0.000	0.001
intervalsDist	0.564	0.027	0.592
mapC	10.094	0.273	10.408
normICE	0.001	0.000	0.000
normLGF	0.000	0.000	0.001
pca.hic	2.391	0.808	2.705
removeIntervals	0.419	0.008	0.427
setGenomicFeatures	0.001	0.000	0.001
setIntervalScale	2.817	0.033	2.853