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: 2017-10-18 00:35:57 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:43:31 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 454.1 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

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### Running command:
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###   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
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/HiTC.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 52.33   0.45   53.86
mapC                 4.77   0.36    5.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
directionalityIndex 52.81   0.30   53.13
HTCexp-class         4.94   0.13    5.07
* 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	4.48	0.16	4.64
HTCexp-class	4.41	0.28	4.69
HTClist-class	0.78	0.00	0.78
Nora_5C	0.19	0.03	0.22
binningC	0.84	0.02	0.85
directionalityIndex	52.33	0.45	53.86
discretize	0	0	0
export.my5C	0	0	0
exportC	0	0	0
extractRegion	0.47	0.00	0.47
getAnnotatedRestrictionSites	0	0	0
getExpectedCounts	2.38	0.27	2.64
getPearsonMap	0.90	0.04	0.95
getRestrictionFragmentsPerChromosome	0	0	0
import.my5C	0.07	0.00	0.06
importC	0	0	0
intervalsDist	0.57	0.06	0.65
mapC	4.77	0.36	5.12
normICE	0	0	0
normLGF	0.01	0.00	0.02
pca.hic	0.57	0.00	0.56
removeIntervals	0.22	0.02	0.23
setGenomicFeatures	0	0	0
setIntervalScale	0.56	0.03	0.59

name	user	system	elapsed
CQC	4.53	0.17	4.82
HTCexp-class	4.94	0.13	5.07
HTClist-class	1	0	1
Nora_5C	0.17	0.01	0.18
binningC	1.12	0.02	1.14
directionalityIndex	52.81	0.30	53.13
discretize	0	0	0
export.my5C	0	0	0
exportC	0	0	0
extractRegion	0.47	0.00	0.46
getAnnotatedRestrictionSites	0	0	0
getExpectedCounts	2.20	0.29	2.50
getPearsonMap	0.7	0.0	0.7
getRestrictionFragmentsPerChromosome	0	0	0
import.my5C	0.07	0.00	0.07
importC	0	0	0
intervalsDist	0.31	0.02	0.32
mapC	3.97	0.33	4.30
normICE	0	0	0
normLGF	0	0	0
pca.hic	0.58	0.00	0.58
removeIntervals	0.28	0.02	0.30
setGenomicFeatures	0	0	0
setIntervalScale	0.80	0.01	0.81