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CHECK report for GEM on tokay1

This page was generated on 2019-04-13 11:26:47 -0400 (Sat, 13 Apr 2019).

Package 586/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEM 1.8.0
Hong Pan
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GEM
Branch: RELEASE_3_8
Last Commit: 79d822c
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GEM
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GEM_1.8.0.tar.gz
StartedAt: 2019-04-13 02:25:33 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:27:54 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 140.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GEM.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GEM_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GEM.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/RtmpKu6VhD/R.INSTALL10fc6f1325d6/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-3.8-bioc/tmpdir/RtmpKu6VhD/R.INSTALL10fc6f1325d6/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-3.8-bioc/tmpdir/RtmpKu6VhD/R.INSTALL10fc6f1325d6/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-3.8-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 5.96    1.1    7.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GEM_GxEmodel 5.92   0.95    6.88
* 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-3.8-bioc/meat/GEM.Rcheck/00check.log'
for details.



Installation output

GEM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GEM_1.8.0.tar.gz && rm -rf GEM.buildbin-libdir && mkdir GEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GEM.buildbin-libdir GEM_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GEM_1.8.0.zip && rm GEM_1.8.0.tar.gz GEM_1.8.0.zip
###
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  % 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  259k  100  259k    0     0  5871k      0 --:--:-- --:--:-- --:--:-- 6496k

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-3.8-bioc/tmpdir/RtmpKu6VhD/R.INSTALL10fc6f1325d6/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-3.8-bioc/tmpdir/RtmpKu6VhD/R.INSTALL10fc6f1325d6/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-3.8-bioc/tmpdir/RtmpKu6VhD/R.INSTALL10fc6f1325d6/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
In R CMD INSTALL

install for x64

* installing *source* package 'GEM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEM' as GEM_1.8.0.zip
* DONE (GEM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GEM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GEM.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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:  0.12  seconds 


RUNIT TEST PROTOCOL -- Sat Apr 13 02:27:41 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 
   7.14    1.34    8.64 

GEM.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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:  0.03  seconds 
100.00% done, 144 methQTL
Analysis done in:  0.06  seconds 
100.00% done, 9 cpg-snp pairs
Analysis done in:  0.11  seconds 


RUNIT TEST PROTOCOL -- Sat Apr 13 02:27:50 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 
   6.90    1.28    8.26 

Example timings

GEM.Rcheck/examples_i386/GEM-Ex.timings

nameusersystemelapsed
GEM-package000
GEM_Emodel0.190.040.68
GEM_GUI000
GEM_GWASmodel0.330.070.53
GEM_Gmodel0.380.000.47
GEM_GxEmodel5.961.107.38
SlicedData-class000

GEM.Rcheck/examples_x64/GEM-Ex.timings

nameusersystemelapsed
GEM-package000
GEM_Emodel0.190.070.32
GEM_GUI000
GEM_GWASmodel0.290.040.34
GEM_Gmodel0.210.050.25
GEM_GxEmodel5.920.956.88
SlicedData-class000