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CHECK report for GGBase on tokay2

This page was generated on 2019-10-16 12:21:49 -0400 (Wed, 16 Oct 2019).

Package 674/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGBase 3.46.0
VJ Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GGBase
Branch: RELEASE_3_9
Last Commit: e700de6
Last Changed Date: 2019-05-02 11:53:10 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GGBase
Version: 3.46.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GGBase_3.46.0.tar.gz
StartedAt: 2019-10-16 04:03:14 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:09:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 371.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GGBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GGBase_3.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GGBase.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '3.46.0'
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
MAFfilter 6.69   0.93    9.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
MAFfilter 5.37   0.74    6.12
plot_EvG  4.88   0.13    5.00
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GGBase.Rcheck/00check.log'
for details.

Installation output

GGBase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GGBase_3.46.0.tar.gz && rm -rf GGBase.buildbin-libdir && mkdir GGBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GGBase.buildbin-libdir GGBase_3.46.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GGBase_3.46.0.zip && rm GGBase_3.46.0.tar.gz GGBase_3.46.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  217k  100  217k    0     0  3140k      0 --:--:-- --:--:-- --:--:-- 3504k

install for i386

* installing *source* package 'GGBase' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GGBase'
    finding HTML links ... done
    MAFfilter                               html  
    finding level-2 HTML links ... done

    clipPCs                                 html  
    externalize                             html  
    make_smlSet                             html  
    plot_EvG                                html  
    rsid-class                              html  
    smlSet-class                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GGBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGBase' as GGBase_3.46.0.zip
* DONE (GGBase)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GGBase' successfully unpacked and MD5 sums checked

Tests output

GGBase.Rcheck/tests_i386/MAFfilter.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
  13.50    1.45   14.93

GGBase.Rcheck/tests_x64/MAFfilter.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
  17.03    1.17   18.18

GGBase.Rcheck/tests_i386/make.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
  11.96    1.51   13.48

GGBase.Rcheck/tests_x64/make.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
  15.82    1.20   17.04

GGBase.Rcheck/tests_i386/plot_EvG.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 object is masked from 'package:Matrix':

    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, basename, cbind, 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, 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


Attaching package: 'IRanges'

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

    windows



> 
> proc.time()
   user  system elapsed 
  12.35    1.37   13.71

GGBase.Rcheck/tests_x64/plot_EvG.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 object is masked from 'package:Matrix':

    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, basename, cbind, 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, 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


Attaching package: 'IRanges'

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

    windows



> 
> proc.time()
   user  system elapsed 
  16.73    1.40   18.14

Example timings

GGBase.Rcheck/examples_i386/GGBase-Ex.timings

nameusersystemelapsed
MAFfilter6.690.939.81
clipPCs000
externalize000
make_smlSet4.210.074.26
plot_EvG4.340.174.52
rsid-class000
smlSet-class000

GGBase.Rcheck/examples_x64/GGBase-Ex.timings

nameusersystemelapsed
MAFfilter5.370.746.12
clipPCs000
externalize000
make_smlSet3.820.043.87
plot_EvG4.880.135.00
rsid-class000
smlSet-class000