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BioC 3.6: CHECK report for gwascat on veracruz1

This page was generated on 2017-08-16 13:42:43 -0400 (Wed, 16 Aug 2017).

Package 617/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwascat 2.9.1
VJ Carey
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gwascat
Last Changed Rev: 130494 / Revision: 131943
Last Changed Date: 2017-06-18 11:13:08 -0400 (Sun, 18 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gwascat
Version: 2.9.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gwascat_2.9.1.tar.gz
StartedAt: 2017-08-16 04:12:14 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:20:17 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 482.8 seconds
RetCode: 0
Status:  OK 
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gwascat_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/gwascat.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.9.1’
* 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 ‘gwascat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 38.7Mb
  sub-directories of 1Mb or more:
    data     30.9Mb
    obo       3.0Mb
    olddata   2.2Mb
    tab       1.1Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildq: no visible global function definition for 'read.delim'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'snpsBySeqname'
lo38to19: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'data'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible global function definition for
  'read.delim'
makeCurrentGwascat: no visible global function definition for 'data'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat: no visible global function definition for
  'sessionInfo'
makeCurrentGwascat.legacy: no visible global function definition for
  'read.delim'
makeCurrentGwascat.legacy: no visible global function definition for
  'data'
makeCurrentGwascat.legacy: no visible binding for global variable
  'si.hs.38'
snpGenos: no visible global function definition for 'getSNPlocs'
tfilt: no visible binding for global variable 'phr'
tpad: no visible binding for global variable 'phr'
traitsManh: no visible binding for global variable 'PVALUE_MLOG'
variantProps: no visible binding for global variable 'gwrngs'
Undefined global functions or variables:
  PVALUE_MLOG data getSNPlocs gwrngs gwrngs19 phr read.delim
  sessionInfo si.hs.37 si.hs.38 snpsBySeqname
Consider adding
  importFrom("utils", "data", "read.delim", "sessionInfo")
to your NAMESPACE file.
* 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 ... NOTE
  Note: found 6 marked Latin-1 strings
  Note: found 1 marked UTF-8 string
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 14.881  0.070  15.417
gwcex2gviz        7.762  0.194   8.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
* 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-3.6-bioc/meat/gwascat.Rcheck/00check.log’
for details.


gwascat.Rcheck/00install.out:

* installing *source* package ‘gwascat’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (gwascat)

gwascat.Rcheck/gwascat-Ex.timings:

nameusersystemelapsed
bindcadd_snv0.0000.0000.001
gwascat-package0.0000.0010.001
gwastagger2.6820.0262.770
gwaswloc-class0.0020.0000.003
gwcex2gviz7.7620.1948.285
gwdf_2012_02_020.0010.0000.001
ldtagr1.0650.0261.132
locon60.0330.0040.037
makeCurrentGwascat0.0010.0000.001
obo2graphNEL0.2450.0050.263
riskyAlleleCount14.881 0.07015.417
topTraits0.4240.0070.441
traitsManh2.5280.0242.664