GOTHiC 1.6.0
Borbala Mifsud
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GOTHiC | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOTHiC_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GOTHiC.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.6.0’
* 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 ... [22s/22s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘S4Vectors::Position’ by ‘ggplot2::Position’ when loading ‘GOTHiC’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/GOTHiC.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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.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’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [77s/88s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOTHiC 42.650 2.478 55.818
GOTHiChicup 12.385 0.294 12.862
pairReads 6.737 0.107 6.871
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.
* installing *source* package ‘GOTHiC’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘S4Vectors::Position’ by ‘ggplot2::Position’ when loading ‘GOTHiC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘S4Vectors::Position’ by ‘ggplot2::Position’ when loading ‘GOTHiC’
* DONE (GOTHiC)