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BioC 3.1: CHECK report for GenomicInteractions on zin2

This page was generated on 2015-10-09 09:26:26 -0700 (Fri, 09 Oct 2015).

Package 399/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicInteractions
Version: 1.2.3
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.2.3.tar.gz
StartedAt: 2015-10-09 01:42:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:46:22 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 222.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicInteractions.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [12s/18s] OK
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    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 ... [10s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [8s/10s]
 [8s/10s] 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.


GenomicInteractions.Rcheck/00install.out:

* 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)

GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings:

nameusersystemelapsed
GenomicInteractions-class0.1900.0030.280
GenomicInteractions0.1660.0000.233
annotateInteractions0.0400.0000.079
calculateDistances0.3620.0000.502
categoriseInteractions0.0420.0000.054
getters0.1360.0070.173
makeGenomicInteractionsFromFile1.3200.0281.914
plotCisTrans0.4580.0040.508
plotCounts0.2460.0150.365
plotDists0.1700.0120.282
plotInteractionAnnotations0.1800.0000.248
plotSummaryStats0.5690.0010.706
setters0.1350.0000.206
viewPoint0.0000.0000.001