Package: GOTHiC

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOTHiC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOTHiC_1.18.1.tar.gz

StartedAt: 2019-04-16 00:22:28 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:27:53 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 324.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GOTHiC.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOTHiC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOTHiC_1.18.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GOTHiC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GOTHiC’ 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
* 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 ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’
':::' call which should be '::': ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.binInteractions: no visible binding for global variable ‘chr1’
.binInteractions: no visible binding for global variable ‘chr2’
.binInteractions: no visible binding for global variable ‘locus1’
.binInteractions: no visible binding for global variable ‘locus2’
.binomialHiC: no visible binding for global variable ‘resGR’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘frequencies’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘int1’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘int2’
.binomialHiC: no visible binding for global variable ‘V1’
.binomialHiC: no visible binding for global variable ‘int1’
.binomialHiC: no visible binding for global variable ‘int2’
.binomialHiC: no visible binding for global variable ‘frequencies’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘binom.test’
.binomialHiC: no visible global function definition for ‘p.adjust’
.binomialHiC: no visible binding for global variable ‘pvalue’
.binomialHiC: no visible global function definition for ‘x11’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘pdf’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘dev.off’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘frequencies’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘int1’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘int2’
.binomialHiChicup: no visible binding for global variable ‘V1’
.binomialHiChicup: no visible binding for global variable ‘int1’
.binomialHiChicup: no visible binding for global variable ‘int2’
.binomialHiChicup: no visible binding for global variable ‘frequencies’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘binom.test’
.binomialHiChicup: no visible global function definition for ‘p.adjust’
.binomialHiChicup: no visible binding for global variable ‘pvalue’
.binomialHiChicup: no visible global function definition for ‘x11’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘pdf’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘dev.off’
.findOverlaps.circle: no visible global function definition for
  ‘IntervalTree’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘isCircular’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘seqlengths’
.getHindIIIsitesFromHicup: no visible global function definition for
  ‘read.table’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘install.packages’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘seqlengths’
.importHicup: no visible global function definition for ‘read.table’
.onlyPairing: no visible global function definition for ‘read.table’
.onlyPairing: no visible global function definition for ‘ScanBamParam’
GOTHiC: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19’
GOTHiC: no visible binding for global variable ‘filtered’
GOTHiC: no visible binding for global variable ‘interactingLoci’
mapReadsToRestrictionSites: no visible binding for global variable
  ‘resGR’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19 IntervalTree ScanBamParam V1 binom.test
  chr1 chr2 dev.off filtered frequencies install.packages int1 int2
  interactingLoci isCircular locus1 locus2 p.adjust pdf pvalue
  read.table resGR seqlengths x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "x11")
  importFrom("stats", "binom.test", "p.adjust")
  importFrom("utils", "install.packages", "read.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOTHiC      44.234  4.725  47.102
GOTHiChicup 14.566  1.313  14.778
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GOTHiC
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GOTHiC’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOTHiC)

name	user	system	elapsed
GOTHiC	44.234	4.725	47.102
GOTHiChicup	14.566	1.313	14.778
filtered	0.103	0.010	0.115
mapReadsToRestrictionSites	2.029	0.122	2.171
pairReads	2.133	0.050	2.211