Back to the "Multiple platform build/check report" A  B  C  D  E [F] G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for FunciSNP on zin2

This page was generated on 2014-10-08 08:49:32 -0700 (Wed, 08 Oct 2014).

Package 303/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FunciSNP 1.6.0
Simon G. Coetzee
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/FunciSNP
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 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 

Summary

Package: FunciSNP
Version: 1.6.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings FunciSNP_1.6.0.tar.gz
StartedAt: 2014-10-07 23:41:48 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:47:32 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 344.2 seconds
RetCode: 0
Status:  OK 
CheckDir: FunciSNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings FunciSNP_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/FunciSNP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FunciSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FunciSNP’ 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 ‘FunciSNP’ can be installed ... [32s/32s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘AnnotationDbi’ ‘GenomicRanges’ ‘org.Hs.eg.db’
  All declared Imports should be used.
':::' calls which should be '::':
  ‘Rsamtools:::close.TabixFile’ ‘Rsamtools:::isOpen’
  ‘Rsamtools:::open.TabixFile’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AnnotateSummary: no visible binding for '<<-' assignment to ‘txdb’
AnnotateSummary: no visible binding for global variable ‘txdb’
FunciSNPplot: no visible binding for global variable ‘R.squared’
FunciSNPplot: no visible binding for global variable ‘r.2’
FunciSNPplot: no visible binding for global variable
  ‘distance.from.tag’
FunciSNPplot: no visible binding for global variable ‘variable’
FunciSNPplot: no visible binding for global variable ‘sig’
FunciSNPplot: no visible binding for global variable ‘value’
* 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 ... [23s/23s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/FunciSNP.Rcheck/00check.log’
for details.

FunciSNP.Rcheck/00install.out:

* installing *source* package ‘FunciSNP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FunciSNP)

FunciSNP.Rcheck/FunciSNP-Ex.timings:

nameusersystemelapsed
CorrelatedSNPs-class0.0000.0000.002
FunciSNP-package1.2370.0401.279
FunciSNPAnnotateSummary0.5040.0080.514
FunciSNPbed0.5200.0120.531
FunciSNPidsFromSummary0.0040.0000.000
FunciSNPplot1.5360.0361.770
FunciSNPsummaryOverlaps0.9200.0160.981
FunciSNPtable1.9880.1522.162
TSList-class0.0000.0000.002
TagSNP-class0.0000.0000.001
getFSNPs0.5680.0440.610