BioC 2.14: CHECK report for HiTC on petty

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 22:29:50 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:39:48 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 597.8 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-darwin10.8.0 (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 ... [45s/47s] 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 ... [110s/108s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              19.268  0.581  20.096
CQC               12.122  0.255  12.586
binningC          11.940  0.151  12.137
HTClist-class      8.012  1.623   9.022
HTCexp-class       8.895  0.297   9.226
getExpectedCounts  6.145  0.859   6.445
pca.hic            4.503  1.739   5.519
setIntervalScale   5.371  0.065   5.443
* 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	12.122	0.255	12.586
HTCexp-class	8.895	0.297	9.226
HTClist-class	8.012	1.623	9.022
Nora_5C	0.417	0.013	0.473
binningC	11.940	0.151	12.137
discretize	0.001	0.000	0.001
export.my5C	0.001	0.000	0.002
exportC	0.001	0.000	0.001
extractRegion	1.133	0.014	1.148
getAnnotatedRestrictionSites	0.001	0.000	0.002
getExpectedCounts	6.145	0.859	6.445
import.my5C	0.642	0.010	0.656
importC	0.001	0.000	0.002
intervalsDist	1.408	0.031	1.446
mapC	19.268	0.581	20.096
normICE	0.001	0.000	0.002
normLGF	0.002	0.000	0.003
pca.hic	4.503	1.739	5.519
removeIntervals	0.771	0.023	0.797
setGenomicFeatures	0.002	0.001	0.003
setIntervalScale	5.371	0.065	5.443