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BioC 3.4: CHECK report for gQTLBase on malbec1

This page was generated on 2017-04-15 16:12:38 -0400 (Sat, 15 Apr 2017).

Package 553/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLBase 1.6.0
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/gQTLBase
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: gQTLBase
Version: 1.6.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gQTLBase_1.6.0.tar.gz
StartedAt: 2017-04-14 23:01:36 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:05:44 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 248.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gQTLBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gQTLBase_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/gQTLBase.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLBase/DESCRIPTION’ ... OK
* this is package ‘gQTLBase’ 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 ‘gQTLBase’ can be installed ... OK
* checking installed package size ... OK
* 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
.describeStore: no visible global function definition for ‘getJobInfo’
.extractByProbes: no visible binding for global variable ‘x’
.extractByRanges: no visible global function definition for
  ‘subsetByOverlaps’
.extractByRanges: no visible binding for global variable ‘x’
DFstoreToFf: no visible binding for global variable ‘x’
cb2range: no visible global function definition for ‘select’
cb2range: no visible global function definition for ‘IRanges’
dendroReduce.bj: no visible global function definition for ‘batchMap’
dendroReduce.fe: no visible binding for global variable ‘i’
describeStore.old: no visible global function definition for ‘hist’
ffapp2: no visible global function definition for ‘as.ff’
ffapp2: no visible global function definition for ‘appendLevels’
ffapp2: no visible global function definition for ‘as.which’
mergeGWhits: no visible global function definition for ‘genome’
storeApply: no visible binding for global variable ‘x’
storeApply2: no visible binding for global variable ‘x’
storeToFf: no visible binding for global variable ‘x’
show,storeDescription: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  IRanges appendLevels as.ff as.which batchMap genome getJobInfo hist i
  median select subsetByOverlaps x
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: ufeatByTiling.Rd:50-52: Dropping empty section \seealso
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
storeApply      24.524  0.192  25.652
mergeCIstates    7.140  0.068   7.931
extractByProbes  5.928  0.056   6.381
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘BiocParallel’
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/gQTLBase.Rcheck/00check.log’
for details.


gQTLBase.Rcheck/00install.out:

* installing *source* package ‘gQTLBase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gQTLBase)

gQTLBase.Rcheck/gQTLBase-Ex.timings:

nameusersystemelapsed
ciseStore-class0.8280.0000.892
describeStore000
extractByProbes5.9280.0566.381
mergeCIstates7.1400.0687.931
storeApply24.524 0.19225.652
storeMapResults0.0000.0000.001
storeToFf1.3920.0081.404
ufeatByTiling000