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BioC 3.2: CHECK report for HiTC on zin1

This page was generated on 2016-04-23 10:12:25 -0700 (Sat, 23 Apr 2016).

Package 497/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.14.0
Nicolas Servant
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/HiTC
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


HiTC.Rcheck/00install.out:

* 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)

HiTC.Rcheck/HiTC-Ex.timings:

nameusersystemelapsed
CQC3.7170.0363.771
HTCexp-class3.2660.0243.305
HTClist-class0.9830.0361.018
Nora_5C0.2080.0040.212
binningC1.6690.0081.676
directionalityIndex40.507 0.22540.873
discretize0.0010.0000.000
export.my5C0.0010.0000.001
exportC000
extractRegion0.4170.0040.421
getAnnotatedRestrictionSites0.0010.0000.001
getExpectedCounts2.2100.0872.306
getRestrictionFragmentsPerChromosome0.0010.0000.001
import.my5C0.0690.0080.077
importC0.0010.0000.001
intervalsDist0.2860.0030.290
mapC3.9590.0153.980
normICE0.0010.0000.001
normLGF0.0000.0000.001
pca.hic0.530.000.53
removeIntervals0.2460.0000.247
setGenomicFeatures0.0010.0000.000
setIntervalScale1.0920.0031.097