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CHECK report for gQTLBase on tokay1

This page was generated on 2018-04-12 13:25:28 -0400 (Thu, 12 Apr 2018).

Package 610/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLBase 1.10.0
VJ Carey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/gQTLBase
Branch: RELEASE_3_6
Last Commit: f493b38
Last Changed Date: 2017-10-30 12:40:47 -0400 (Mon, 30 Oct 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: gQTLBase
Version: 1.10.0
Command: rm -rf gQTLBase.buildbin-libdir gQTLBase.Rcheck && mkdir gQTLBase.buildbin-libdir gQTLBase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLBase.buildbin-libdir gQTLBase_1.10.0.tar.gz >gQTLBase.Rcheck\00install.out 2>&1 && cp gQTLBase.Rcheck\00install.out gQTLBase-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gQTLBase.buildbin-libdir --install="check:gQTLBase-install.out" --force-multiarch --no-vignettes --timings gQTLBase_1.10.0.tar.gz
StartedAt: 2018-04-12 00:30:32 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:45:27 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 895.4 seconds
RetCode: 0
Status:  OK  
CheckDir: gQTLBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gQTLBase.buildbin-libdir gQTLBase.Rcheck && mkdir gQTLBase.buildbin-libdir gQTLBase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLBase.buildbin-libdir gQTLBase_1.10.0.tar.gz >gQTLBase.Rcheck\00install.out 2>&1 && cp gQTLBase.Rcheck\00install.out gQTLBase-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gQTLBase.buildbin-libdir --install="check:gQTLBase-install.out" --force-multiarch --no-vignettes --timings gQTLBase_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gQTLBase.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gQTLBase/DESCRIPTION' ... OK
* this is package 'gQTLBase' version '1.10.0'
* 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 '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
* 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
.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
storeApply      28.59   0.64   66.02
extractByProbes  9.36   0.33   11.40
mergeCIstates    9.32   0.31   11.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
storeApply      26.07   0.31   26.39
mergeCIstates    8.85   0.33    9.27
extractByProbes  8.00   0.15    8.15
* 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
'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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/gQTLBase.Rcheck/00check.log'
for details.



Installation output

gQTLBase.Rcheck/00install.out


install for i386

* installing *source* package 'gQTLBase' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gQTLBase'
    finding HTML links ... done
    ciseStore-class                         html  
    describeStore                           html  
    extractByProbes                         html  
    gqtlBase-package                        html  
    mergeCIstates                           html  
    storeApply                              html  
    storeMapResults                         html  
    storeToFf                               html  
    ufeatByTiling                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gQTLBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLBase' as gQTLBase_1.10.0.zip
* DONE (gQTLBase)
In R CMD INSTALL
In R CMD INSTALL

Tests output

gQTLBase.Rcheck/tests_i386/test-all.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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 development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files: 
  1: C:/Users/biocbuild/bbs-3.6-bioc/R/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 -- Thu Apr 12 00:41:20 2018 
*********************************************** 
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 
  13.78    2.14  208.48 

gQTLBase.Rcheck/tests_x64/test-all.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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 development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files: 
  1: C:/Users/biocbuild/bbs-3.6-bioc/R/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 -- Thu Apr 12 00:45:22 2018 
*********************************************** 
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 
  16.17    1.28  241.68 

Example timings

gQTLBase.Rcheck/examples_i386/gQTLBase-Ex.timings

nameusersystemelapsed
ciseStore-class0.690.051.17
describeStore000
extractByProbes 9.36 0.3311.40
mergeCIstates 9.32 0.3111.16
storeApply28.59 0.6466.02
storeMapResults000
storeToFf0.640.060.71
ufeatByTiling000

gQTLBase.Rcheck/examples_x64/gQTLBase-Ex.timings

nameusersystemelapsed
ciseStore-class0.460.050.50
describeStore000
extractByProbes8.000.158.15
mergeCIstates8.850.339.27
storeApply26.07 0.3126.39
storeMapResults000
storeToFf0.580.030.61
ufeatByTiling000