BioC 3.4: CHECK report for HiTC on tokay1

Package: HiTC

Version: 1.18.1

Command: rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.18.1.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.18.1.tar.gz

StartedAt: 2017-04-14 22:59:14 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:05:38 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 384.2 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.18.1.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.18.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/HiTC.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.18.1'
* 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 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
** checking loading without being on the library search path ... 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 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
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 47.66   0.75   51.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
directionalityIndex 43.57   0.33   43.90
CQC                  4.81   0.20    5.21
* 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
  'C:/Users/biocbuild/bbs-3.4-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_1.18.1.zip
* DONE (HiTC)

name	user	system	elapsed
CQC	4.61	0.33	4.93
HTCexp-class	3.78	0.34	4.14
HTClist-class	1.41	0.03	1.44
Nora_5C	0.49	0.05	0.53
binningC	1.40	0.00	1.41
directionalityIndex	47.66	0.75	51.56
discretize	0	0	0
export.my5C	0.01	0.00	0.02
exportC	0	0	0
extractRegion	0.22	0.03	0.25
getAnnotatedRestrictionSites	0	0	0
getExpectedCounts	2.03	0.17	2.20
getPearsonMap	0.57	0.02	0.58
getRestrictionFragmentsPerChromosome	0	0	0
import.my5C	0.06	0.00	0.06
importC	0	0	0
intervalsDist	0.25	0.00	0.25
mapC	3.64	0.27	4.92
normICE	0	0	0
normLGF	0	0	0
pca.hic	0.51	0.00	0.51
removeIntervals	0.24	0.01	0.25
setGenomicFeatures	0	0	0
setIntervalScale	0.64	0.02	0.66

name	user	system	elapsed
CQC	4.81	0.20	5.21
HTCexp-class	3.33	0.18	3.50
HTClist-class	1.32	0.01	1.33
Nora_5C	0.26	0.00	0.26
binningC	0.99	0.00	0.99
directionalityIndex	43.57	0.33	43.90
discretize	0	0	0
export.my5C	0	0	0
exportC	0	0	0
extractRegion	0.26	0.03	0.29
getAnnotatedRestrictionSites	0	0	0
getExpectedCounts	2.04	0.14	2.18
getPearsonMap	0.67	0.02	0.68
getRestrictionFragmentsPerChromosome	0	0	0
import.my5C	0.06	0.00	0.07
importC	0	0	0
intervalsDist	0.31	0.02	0.33
mapC	4.02	0.12	4.14
normICE	0	0	0
normLGF	0	0	0
pca.hic	0.65	0.00	0.66
removeIntervals	0.33	0.00	0.33
setGenomicFeatures	0	0	0
setIntervalScale	1.01	0.02	1.03