BioC 3.2: CHECK report for HiTC on zin1

Package: HiTC

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.14.0.tar.gz

StartedAt: 2016-04-23 01:51:45 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:55:32 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 226.6 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/HiTC.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.14.0’
* 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 ... [16s/16s] 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
getBlocsIndex: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
  definition for ‘seqlevels<-’
isBinned,HTCexp: no visible global function definition for
  ‘countMatches’
* 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 ... [68s/68s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
directionalityIndex 40.507  0.225  40.873
* 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-3.2-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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HiTC)

name	user	system	elapsed
CQC	3.717	0.036	3.771
HTCexp-class	3.266	0.024	3.305
HTClist-class	0.983	0.036	1.018
Nora_5C	0.208	0.004	0.212
binningC	1.669	0.008	1.676
directionalityIndex	40.507	0.225	40.873
discretize	0.001	0.000	0.000
export.my5C	0.001	0.000	0.001
exportC	0	0	0
extractRegion	0.417	0.004	0.421
getAnnotatedRestrictionSites	0.001	0.000	0.001
getExpectedCounts	2.210	0.087	2.306
getRestrictionFragmentsPerChromosome	0.001	0.000	0.001
import.my5C	0.069	0.008	0.077
importC	0.001	0.000	0.001
intervalsDist	0.286	0.003	0.290
mapC	3.959	0.015	3.980
normICE	0.001	0.000	0.001
normLGF	0.000	0.000	0.001
pca.hic	0.53	0.00	0.53
removeIntervals	0.246	0.000	0.247
setGenomicFeatures	0.001	0.000	0.000
setIntervalScale	1.092	0.003	1.097