GOTHiC 1.7.0
Borbala Mifsud
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOTHiC | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GOTHiC_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GOTHiC.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.7.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GOTHiC’ can be installed ... [15s/15s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘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: no visible binding for global variable ‘pvalue’
.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: no visible binding for global variable ‘pvalue’
.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’
.getRestrictionSitesFromBSgenome: no visible global function definition
for ‘biocLite’
.getRestrictionSitesFromBSgenome: no visible global function definition
for ‘seqlengths’
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 V1 biocLite chr1 chr2
filtered frequencies int1 int2 interactingLoci isCircular locus1
locus2 pvalue resGR seqlengths
* 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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOTHiC 46.106 1.044 47.215
GOTHiChicup 7.567 0.148 7.716
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.