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BioC 3.2: CHECK report for FunciSNP on oaxaca

This page was generated on 2015-10-27 17:40:05 -0400 (Tue, 27 Oct 2015).

Package 382/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FunciSNP 1.12.0
Simon G. Coetzee
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/FunciSNP
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FunciSNP
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FunciSNP_1.12.0.tar.gz
StartedAt: 2015-10-27 03:45:10 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:51:29 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 378.8 seconds
RetCode: 0
Status:  OK 
CheckDir: FunciSNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FunciSNP_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/FunciSNP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.0’
* 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 ... [36s/36s] 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.
* 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 global function definition for
  ‘GRangesList’
AnnotateSummary: no visible global function definition for
  ‘elementMetadata’
AnnotateSummary: no visible global function definition for ‘GRanges’
AnnotateSummary: no visible global function definition for ‘RangedData’
AnnotateSummary: no visible binding for global variable ‘lincRNA’
AnnotateSummary: no visible binding for '<<-' assignment to ‘txdb’
AnnotateSummary: no visible binding for global variable ‘refseqgenes’
AnnotateSummary: no visible binding for global variable ‘txdb’
CreateCorrelatedSNPs: no visible global function definition for
  ‘GRangesList’
FilterByFeatures: no visible global function definition for ‘GRanges’
FilterByFeatures: no visible global function definition for
  ‘elementMetadata’
FilterByFeatures: no visible global function definition for
  ‘elementMetadata<-’
FilterByFeatures: no visible global function definition for
  ‘findOverlaps’
FilterByFeatures: no visible global function definition for ‘queryHits’
FilterByFeatures: no visible global function definition for
  ‘GRangesList’
FilterByFeatures: no visible global function definition for
  ‘subjectHits’
FunciSNPbed: no visible global function definition for
  ‘package.version’
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’
PullInVariants: no visible global function definition for ‘GRanges’
SNPSummary: no visible global function definition for ‘elementMetadata’
SNPSummary: no visible global function definition for
  ‘elementMetadata<-’
getFSNPs: no visible global function definition for ‘package.version’
show,TagSNP: no visible global function definition for
  ‘elementMetadata’
* 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 ... [24s/24s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-class0.0030.0010.002
FunciSNP-package1.5570.0461.605
FunciSNPAnnotateSummary0.6230.0160.639
FunciSNPbed0.6490.0400.692
FunciSNPidsFromSummary000
FunciSNPplot1.4870.0771.566
FunciSNPsummaryOverlaps0.1830.0320.216
FunciSNPtable1.7460.2071.955
TSList-class0.0020.0000.002
TagSNP-class0.0010.0010.002
getFSNPs0.1800.0310.212