Package: gQTLBase

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gQTLBase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gQTLBase_1.15.0.tar.gz

StartedAt: 2019-04-09 01:20:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:26:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 371.0 seconds

RetCode: 0

Status:  OK

CheckDir: gQTLBase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gQTLBase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gQTLBase_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gQTLBase.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLBase/DESCRIPTION’ ... OK
* this is package ‘gQTLBase’ version ‘1.15.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
storeApply      28.240  1.062  29.727
extractByProbes  6.406  0.247   6.743
mergeCIstates    4.720  0.338   5.109
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/gQTLBase.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gQTLBase
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘gQTLBase’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gQTLBase)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("gQTLBase")
Loading required package: digest
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: BatchJobs
Loading required package: BBmisc

Attaching package: 'BBmisc'

The following object is masked from 'package:IRanges':

    collapse

The following object is masked from 'package:BiocGenerics':

    normalize

The following object is masked from 'package:base':

    isFALSE

The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files: 
  1: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BatchJobs/etc/BatchJobs_global_config.R
BatchJobs configuration:
  cluster functions: Interactive
  mail.from: 
  mail.to: 
  mail.start: none
  mail.done: none
  mail.error: none
  default.resources: 
  debug: FALSE
  raise.warnings: FALSE
  staged.queries: TRUE
  max.concurrent.jobs: Inf
  fs.timeout: NA
  measure.mem: TRUE

Loading required package: GenomicRanges
building probe:job map...
done.
building range:job map...
done.


RUNIT TEST PROTOCOL -- Tue Apr  9 01:26:11 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gQTLBase RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
250.365 145.368  59.526 

name	user	system	elapsed
ciseStore-class	0.538	0.017	0.560
describeStore	0	0	0
extractByProbes	6.406	0.247	6.743
mergeCIstates	4.720	0.338	5.109
storeApply	28.240	1.062	29.727
storeMapResults	0.001	0.001	0.000
storeToFf	0.631	0.031	0.670
ufeatByTiling	0.001	0.000	0.000