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CHECK report for GGBase on tokay1

This page was generated on 2018-04-12 13:19:12 -0400 (Thu, 12 Apr 2018).

Package 581/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGBase 3.40.0
VJ Carey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GGBase
Branch: RELEASE_3_6
Last Commit: 2bf18cf
Last Changed Date: 2017-10-30 12:39:23 -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 [ WARNINGS ] 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: GGBase
Version: 3.40.0
Command: rm -rf GGBase.buildbin-libdir GGBase.Rcheck && mkdir GGBase.buildbin-libdir GGBase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGBase.buildbin-libdir GGBase_3.40.0.tar.gz >GGBase.Rcheck\00install.out 2>&1 && cp GGBase.Rcheck\00install.out GGBase-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GGBase.buildbin-libdir --install="check:GGBase-install.out" --force-multiarch --no-vignettes --timings GGBase_3.40.0.tar.gz
StartedAt: 2018-04-12 00:23:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:28:55 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 338.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GGBase.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GGBase.buildbin-libdir GGBase.Rcheck && mkdir GGBase.buildbin-libdir GGBase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGBase.buildbin-libdir GGBase_3.40.0.tar.gz >GGBase.Rcheck\00install.out 2>&1 && cp GGBase.Rcheck\00install.out GGBase-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GGBase.buildbin-libdir --install="check:GGBase-install.out" --force-multiarch --no-vignettes --timings GGBase_3.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GGBase.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 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.40.0'
* 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 'GGBase' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/MAFfilter.Rd:37: missing file link 'col.summary'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/clipPCs.Rd:27: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/clipPCs.Rd:31: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/make_smlSet.Rd:22: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:35: missing file link 'AssayData-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:37: missing file link 'AnnotatedDataFrame-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:41: missing file link 'MIAxE-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:44: missing file link 'eSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:65: missing file link 'nsFilter,ExpressionSet-method'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GGBase.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
getSS: no visible global function definition for 'installed.packages'
Undefined global functions or variables:
  installed.packages
Consider adding
  importFrom("utils", "installed.packages")
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 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
MAFfilter 4.11   0.31    9.70
plot_EvG  3.69   0.13    5.72
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'MAFfilter.R'
  Running 'make.R'
  Running 'plot_EvG.R'
 OK
** running tests for arch 'x64' ...
  Running 'MAFfilter.R'
  Running 'make.R'
  Running 'plot_EvG.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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GGBase.Rcheck/00check.log'
for details.

Installation output

GGBase.Rcheck/00install.out


install for i386

* installing *source* package 'GGBase' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GGBase'
    finding HTML links ... done
    MAFfilter                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/MAFfilter.Rd:37: missing file link 'col.summary'
    clipPCs                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/clipPCs.Rd:27: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/clipPCs.Rd:31: missing file link 'RangedSummarizedExperiment'
    externalize                             html  
    make_smlSet                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/make_smlSet.Rd:22: missing file link 'ExpressionSet-class'
    plot_EvG                                html  
    rsid-class                              html  
    finding level-2 HTML links ... done

    smlSet-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:35: missing file link 'AssayData-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:37: missing file link 'AnnotatedDataFrame-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:41: missing file link 'MIAxE-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:44: missing file link 'eSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpS8zzE9/R.INSTALL950dcb32a/GGBase/man/smlSet-class.Rd:65: missing file link 'nsFilter,ExpressionSet-method'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GGBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGBase' as GGBase_3.40.0.zip
* DONE (GGBase)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GGBase.Rcheck/tests_i386/MAFfilter.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.

> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20")
+  nsnp = ncol(smList(s20)[[1]])
+  s20f = MAFfilter(s20, lower=.1)
+  nsnp2 = ncol(smList(s20f)[[1]])
+  ( nsnp == 119921 & nsnp2 == 46755 )
+ }
[1] FALSE
> 
> proc.time()
   user  system elapsed 
  13.56    0.67   14.21

GGBase.Rcheck/tests_x64/MAFfilter.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.

> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20")
+  nsnp = ncol(smList(s20)[[1]])
+  s20f = MAFfilter(s20, lower=.1)
+  nsnp2 = ncol(smList(s20f)[[1]])
+  ( nsnp == 119921 & nsnp2 == 46755 )
+ }
[1] FALSE
> 
> proc.time()
   user  system elapsed 
  10.87    0.50   11.37

GGBase.Rcheck/tests_i386/make.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.

> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20")
+  remk = make_smlSet( as(s20, "ExpressionSet"), smList(s20) )
+  validObject(s20) & validObject(remk)
+ }
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  12.85    0.84   13.68

GGBase.Rcheck/tests_x64/make.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.

> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20")
+  remk = make_smlSet( as(s20, "ExpressionSet"), smList(s20) )
+  validObject(s20) & validObject(remk)
+ }
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  14.59    0.73   15.32

GGBase.Rcheck/tests_i386/plot_EvG.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.

> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20")
+  plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
+ }

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:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    expand

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

    expand.grid



> 
> proc.time()
   user  system elapsed 
  11.04    0.57   11.62

GGBase.Rcheck/tests_x64/plot_EvG.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.

> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20")
+  plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
+ }

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:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    expand

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

    expand.grid



> 
> proc.time()
   user  system elapsed 
  12.32    0.56   12.87

Example timings

GGBase.Rcheck/examples_i386/GGBase-Ex.timings

nameusersystemelapsed
MAFfilter4.110.319.70
clipPCs000
externalize000
make_smlSet3.550.063.61
plot_EvG3.690.135.72
rsid-class000
smlSet-class000

GGBase.Rcheck/examples_x64/GGBase-Ex.timings

nameusersystemelapsed
MAFfilter4.330.304.62
clipPCs000
externalize000
make_smlSet3.860.063.92
plot_EvG3.830.174.00
rsid-class000
smlSet-class000