GenomicInteractions 1.2.3
Malcolm Perry , Liz Ing-Simmons
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomicInteractions | | Last Changed Rev: 108820 / Revision: 109384 | | Last Changed Date: 2015-09-24 12:33:35 -0700 (Thu, 24 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | 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 GenomicInteractions_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.2.3’
* 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 ‘GenomicInteractions’ can be installed ... [24s/24s] OK
* checking installed package size ... NOTE
installed size is 10.6Mb
sub-directories of 1Mb or more:
doc 1.9Mb
extdata 7.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 objects imported by ':::' calls:
‘BiocGenerics:::updateS4’ ‘GenomeInfoDb:::getDanglingSeqlevels’
‘GenomeInfoDb:::makeNewSeqnames’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
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
get_binom_ligation_threshold: no visible binding for global variable
‘Bin’
get_binom_ligation_threshold: no visible binding for global variable
‘SameStrand’
get_binom_ligation_threshold: no visible binding for global variable
‘Total’
get_binom_ligation_threshold: no visible binding for global variable
‘OppStrand’
get_binom_ligation_threshold: no visible binding for global variable
‘OppPercent’
get_binom_ligation_threshold: no visible binding for global variable
‘p.value’
get_self_ligation_threshold: no visible binding for global variable
‘Bin’
get_self_ligation_threshold: no visible binding for global variable
‘SameStrand’
get_self_ligation_threshold: no visible binding for global variable
‘Total’
get_self_ligation_threshold: no visible binding for global variable
‘OppStrand’
get_self_ligation_threshold: no visible binding for global variable
‘log2Ratio’
plotCisTrans: no visible binding for global variable ‘category’
plotCisTrans: no visible binding for global variable ‘ymax’
plotCisTrans: no visible binding for global variable ‘ymin’
plotCisTrans: no visible binding for global variable ‘label’
plotCounts: no visible binding for global variable ‘Var1’
plotCounts: no visible binding for global variable ‘Freq’
plotDists: no visible binding for global variable ‘Distance’
plotInteractionAnnotations: no visible binding for global variable
‘fraction’
plotInteractionAnnotations: no visible binding for global variable
‘category’
plotInteractionAnnotations: no visible binding for global variable
‘ymax’
plotInteractionAnnotations: no visible binding for global variable
‘ymin’
plotInteractionAnnotations: no visible binding for global variable
‘label’
plotRegion,GenomicInteractions-GRanges-list: no visible global function
definition for ‘count’
* 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 ... [20s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/16s]
[17s/17s] OK
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.
* installing *source* package ‘GenomicInteractions’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘print’ from package ‘base’ in package ‘GenomicInteractions’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GenomicInteractions)