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BioC 3.4: CHECK report for gwascat on tokay1

This page was generated on 2017-04-15 16:17:07 -0400 (Sat, 15 Apr 2017).

Package 576/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwascat 2.6.0
VJ Carey
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/gwascat
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gwascat
Version: 2.6.0
Command: rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.6.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.6.0.tar.gz
StartedAt: 2017-04-14 22:54:47 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:04:17 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 569.5 seconds
RetCode: 0
Status:  OK  
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.6.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/gwascat.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.6.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 'getSNPlocs'
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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
riskyAlleleCount 11.58   0.06   11.64
gwcex2gviz        4.76   0.28    5.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
riskyAlleleCount 13.31   0.11   13.42
gwcex2gviz        7.74   0.19    7.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/gwascat.Rcheck/00check.log'
for details.


gwascat.Rcheck/00install.out:


install for i386

* installing *source* package 'gwascat' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gwascat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gwascat' as gwascat_2.6.0.zip
* DONE (gwascat)

gwascat.Rcheck/examples_i386/gwascat-Ex.timings:

nameusersystemelapsed
bindcadd_snv000
gwascat-package000
gwastagger1.720.061.79
gwaswloc-class000
gwcex2gviz4.760.285.04
gwdf_2012_02_02000
ldtagr0.570.001.13
locon60.030.000.03
makeCurrentGwascat000
obo2graphNEL0.250.020.26
riskyAlleleCount11.58 0.0611.64
topTraits0.890.020.91
traitsManh0.700.010.72

gwascat.Rcheck/examples_x64/gwascat-Ex.timings:

nameusersystemelapsed
bindcadd_snv000
gwascat-package000
gwastagger3.630.053.75
gwaswloc-class0.010.000.01
gwcex2gviz7.740.197.94
gwdf_2012_02_02000
ldtagr0.770.070.84
locon60.020.000.01
makeCurrentGwascat000
obo2graphNEL0.150.020.17
riskyAlleleCount13.31 0.1113.42
topTraits0.320.030.34
traitsManh0.790.000.80