BioC 3.5: CHECK report for HiTC on tokay2

Package: HiTC

Version: 1.20.0

Command: rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.20.0.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.20.0.tar.gz

StartedAt: 2017-08-16 00:30:50 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:38:06 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 436.5 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.20.0.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/HiTC.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiTC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiTC' version '1.20.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'HiTC' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
directionalityIndex: no visible global function definition for
  'subjectHits'
directionalityIndex: no visible global function definition for
  'queryHits'
getBlocsIndex: no visible global function definition for 'Rle'
getExpectedCountsMean: 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<-'
divide,HTCexp-HTCexp: no visible global function definition for
  'queryHits'
divide,HTCexp-HTCexp: no visible global function definition for
  'subjectHits'
isBinned,HTCexp: no visible global function definition for
  'countMatches'
substract,HTCexp-HTCexp: no visible global function definition for
  'queryHits'
substract,HTCexp-HTCexp: no visible global function definition for
  'subjectHits'
Undefined global functions or variables:
  Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
directionalityIndex 52.86   0.57   54.92
mapC                 5.06   0.34    5.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
directionalityIndex 44.95   0.32   45.29
HTCexp-class         5.49   0.08    5.56
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/HiTC.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'HiTC' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'HiTC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiTC' as HiTC_1.20.0.zip
* DONE (HiTC)

name	user	system	elapsed
CQC	4.58	0.14	4.72
HTCexp-class	3.95	0.33	4.30
HTClist-class	1	0	1
Nora_5C	0.22	0.01	0.24
binningC	0.87	0.00	0.87
directionalityIndex	52.86	0.57	54.92
discretize	0	0	0
export.my5C	0	0	0
exportC	0	0	0
extractRegion	0.36	0.01	0.37
getAnnotatedRestrictionSites	0	0	0
getExpectedCounts	1.94	0.23	2.17
getPearsonMap	1.13	0.10	1.22
getRestrictionFragmentsPerChromosome	0	0	0
import.my5C	0.07	0.00	0.07
importC	0	0	0
intervalsDist	0.41	0.00	0.41
mapC	5.06	0.34	5.41
normICE	0	0	0
normLGF	0.02	0.00	0.01
pca.hic	0.78	0.00	0.78
removeIntervals	0.38	0.01	0.39
setGenomicFeatures	0	0	0
setIntervalScale	0.95	0.02	0.97

name	user	system	elapsed
CQC	4.42	0.22	4.78
HTCexp-class	5.49	0.08	5.56
HTClist-class	1.28	0.00	1.28
Nora_5C	0.24	0.00	0.23
binningC	1.48	0.00	1.49
directionalityIndex	44.95	0.32	45.29
discretize	0	0	0
export.my5C	0	0	0
exportC	0	0	0
extractRegion	0.44	0.02	0.45
getAnnotatedRestrictionSites	0	0	0
getExpectedCounts	2.20	0.25	2.45
getPearsonMap	0.63	0.00	0.63
getRestrictionFragmentsPerChromosome	0	0	0
import.my5C	0.06	0.00	0.06
importC	0	0	0
intervalsDist	0.45	0.01	0.47
mapC	3.85	0.18	4.01
normICE	0	0	0
normLGF	0	0	0
pca.hic	0.57	0.00	0.58
removeIntervals	0.25	0.01	0.27
setGenomicFeatures	0	0	0
setIntervalScale	0.61	0.03	0.64