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CHECK report for GEM on tokay2

This page was generated on 2019-04-09 12:26:44 -0400 (Tue, 09 Apr 2019).

Package 609/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEM 1.9.0
Hong Pan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GEM
Branch: master
Last Commit: 9c5cd85
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
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 [ WARNINGS ] 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: GEM
Version: 1.9.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GEM_1.9.0.tar.gz
StartedAt: 2019-04-09 02:53:35 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:55:02 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 86.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GEM.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GEM_1.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEM.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEM' version '1.9.0'
* 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 'GEM' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0SXM2X/R.INSTALLff02ee77fab/GEM/man/SlicedData-class.Rd:89: file link 'rowMeans' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0SXM2X/R.INSTALLff02ee77fab/GEM/man/SlicedData-class.Rd:90: file link 'rowSums' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0SXM2X/R.INSTALLff02ee77fab/GEM/man/SlicedData-class.Rd:91: file link 'colMeans' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEM.Rcheck/00install.out' for details.
* 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 ... OK
* 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
GEM_GxEmodel 6.72   1.08    7.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GEM_GxEmodel 6.07   1.09     7.3
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEM.Rcheck/00check.log'
for details.



Installation output

GEM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GEM_1.9.0.tar.gz && rm -rf GEM.buildbin-libdir && mkdir GEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GEM.buildbin-libdir GEM_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GEM_1.9.0.zip && rm GEM_1.9.0.tar.gz GEM_1.9.0.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  262k  100  262k    0     0  3868k      0 --:--:-- --:--:-- --:--:-- 4304k

install for i386

* installing *source* package 'GEM' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GEM'
    finding HTML links ... done
    GEM-package                             html  
    GEM_Emodel                              html  
    GEM_GUI                                 html  
    GEM_GWASmodel                           html  
    GEM_Gmodel                              html  
    GEM_GxEmodel                            html  
    SlicedData-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0SXM2X/R.INSTALLff02ee77fab/GEM/man/SlicedData-class.Rd:89: file link 'rowMeans' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0SXM2X/R.INSTALLff02ee77fab/GEM/man/SlicedData-class.Rd:90: file link 'rowSums' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0SXM2X/R.INSTALLff02ee77fab/GEM/man/SlicedData-class.Rd:91: file link 'colMeans' in package 'base' does not exist and so has been treated as a topic
** 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 'GEM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEM' as GEM_1.9.0.zip
* DONE (GEM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GEM' successfully unpacked and MD5 sums checked

Tests output

GEM.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("GEM")
100.00% done, 100 CpGs
Analysis done in:  0.05  seconds 
100.00% done, 144 methQTL
Analysis done in:  0.09  seconds 
100.00% done, 9 cpg-snp pairs
Analysis done in:  0.13  seconds 


RUNIT TEST PROTOCOL -- Tue Apr 09 02:54:47 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GEM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   8.17    1.35    9.71 

GEM.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("GEM")
100.00% done, 100 CpGs
Analysis done in:  0.04  seconds 
100.00% done, 144 methQTL
Analysis done in:  0.08  seconds 
100.00% done, 9 cpg-snp pairs
Analysis done in:  0.11  seconds 


RUNIT TEST PROTOCOL -- Tue Apr 09 02:54:57 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GEM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   7.85    1.07    8.96 

Example timings

GEM.Rcheck/examples_i386/GEM-Ex.timings

nameusersystemelapsed
GEM-package000
GEM_Emodel0.300.030.47
GEM_GUI000
GEM_GWASmodel0.440.110.68
GEM_Gmodel0.310.000.31
GEM_GxEmodel6.721.087.87
SlicedData-class000

GEM.Rcheck/examples_x64/GEM-Ex.timings

nameusersystemelapsed
GEM-package000
GEM_Emodel0.220.040.28
GEM_GUI000
GEM_GWASmodel0.320.060.39
GEM_Gmodel0.180.050.22
GEM_GxEmodel6.071.097.30
SlicedData-class000