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CHECK report for GENESIS on tokay1

This page was generated on 2018-04-12 13:25:55 -0400 (Thu, 12 Apr 2018).

Package 549/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.8.1
Matthew P. Conomos , Stephanie M. Gogarten
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GENESIS
Branch: RELEASE_3_6
Last Commit: 9a4284c
Last Changed Date: 2018-01-18 16:19:04 -0400 (Thu, 18 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GENESIS
Version: 2.8.1
Command: rm -rf GENESIS.buildbin-libdir GENESIS.Rcheck && mkdir GENESIS.buildbin-libdir GENESIS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GENESIS.buildbin-libdir GENESIS_2.8.1.tar.gz >GENESIS.Rcheck\00install.out 2>&1 && cp GENESIS.Rcheck\00install.out GENESIS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GENESIS.buildbin-libdir --install="check:GENESIS-install.out" --force-multiarch --no-vignettes --timings GENESIS_2.8.1.tar.gz
StartedAt: 2018-04-12 00:15:04 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:24:57 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 592.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GENESIS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GENESIS.buildbin-libdir GENESIS.Rcheck && mkdir GENESIS.buildbin-libdir GENESIS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GENESIS.buildbin-libdir GENESIS_2.8.1.tar.gz >GENESIS.Rcheck\00install.out 2>&1 && cp GENESIS.Rcheck\00install.out GENESIS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GENESIS.buildbin-libdir --install="check:GENESIS-install.out" --force-multiarch --no-vignettes --timings GENESIS_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GENESIS.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 'GENESIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GENESIS' version '2.8.1'
* 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 'GENESIS' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'survey:::saddle'
  See the note in ?`:::` about the use of this operator.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
assocTestMM 12.47   0.80   13.44
varCompCI   12.47   0.64   13.10
fitNullMM   11.58   0.52   12.09
pcrelate    11.36   0.61   11.97
admixMapMM   8.69   0.70    9.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
fitNullMM   16.92   0.85   17.79
varCompCI   15.06   0.52   15.58
pcrelate    14.61   0.63   15.23
assocTestMM 12.06   0.73   12.86
admixMapMM   9.87   0.59   10.98
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GENESIS.Rcheck/00check.log'
for details.

Installation output

GENESIS.Rcheck/00install.out


install for i386

* installing *source* package 'GENESIS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GENESIS'
    finding HTML links ... done
    GENESIS-package                         html  
    HapMap_ASW_MXL_KINGmat                  html  
    admixMapMM                              html  
    finding level-2 HTML links ... done

    assocTestMM                             html  
    assocTestSeq                            html  
    assocTestSeqWindow                      html  
    fitNullMM                               html  
    fitNullReg                              html  
    king2mat                                html  
    pcair                                   html  
    pcairPartition                          html  
    pcrelate                                html  
    pcrelateMakeGRM                         html  
    pcrelateReadInbreed                     html  
    pcrelateReadKinship                     html  
    plot.pcair                              html  
    varCompCI                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GENESIS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENESIS' as GENESIS_2.8.1.zip
* DONE (GENESIS)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GENESIS.Rcheck/tests_i386/runTests.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("GENESIS")
Loading required package: SeqArray
Loading required package: gdsfmt
Loading required package: Biobase
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

Welcome to Bioconductor

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


Attaching package: 'GWASTools'

The following objects are masked from 'package:SeqVarTools':

    alleleFrequency, duplicateDiscordance, getGenotype, mendelErr

SNPRelate
# of selected variants: 100
# of selected samples: 90
# of selected variants: 1,348
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
Reading in Phenotype and Covariate Data...
Fitting Model with 90 Samples
Loading required namespace: survey
Loading required namespace: CompQuadForm
Reading .kin0 file...
Reading .kin file...
Determining Unique Individual IDs from KING Output...
Checking Provided Individual IDs
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 5.844 secs
...SNP Block 2 of 2 Completed - 5.281 secs
Performing Small Sample Correction...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 6.365 secs
...SNP Block 2 of 2 Completed - 5.974 secs
Performing Small Sample Correction...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Creating GDS file for Allele Frequency Estimates:
Estimating Allele Frequencies...
...SNP Block 1 of 2 Completed - 0.7163 secs
...SNP Block 2 of 2 Completed - 0.5781 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 5.594 secs
...SNP Block 2 of 2 Completed - 6.453 secs
Performing Small Sample Correction...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Creating GDS file for Allele Frequency Estimates:
Estimating Allele Frequencies...
...SNP Block 1 of 2 Completed - 0.6563 secs
...SNP Block 2 of 2 Completed - 0.6875 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 6.142 secs
...SNP Block 2 of 2 Completed - 6.539 secs
Performing Small Sample Correction...


RUNIT TEST PROTOCOL -- Thu Apr 12 00:22:44 2018 
*********************************************** 
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GENESIS RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  88.53    4.03  103.34

GENESIS.Rcheck/tests_x64/runTests.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("GENESIS")
Loading required package: SeqArray
Loading required package: gdsfmt
Loading required package: Biobase
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

Welcome to Bioconductor

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


Attaching package: 'GWASTools'

The following objects are masked from 'package:SeqVarTools':

    alleleFrequency, duplicateDiscordance, getGenotype, mendelErr

SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
# of selected variants: 100
# of selected samples: 90
# of selected variants: 1,348
Hint: it is suggested to call `snpgdsOpen' to open a SNP GDS file instead of `openfn.gds'.
Reading in Phenotype and Covariate Data...
Fitting Model with 90 Samples
Loading required namespace: survey
Loading required namespace: CompQuadForm
Reading .kin0 file...
Reading .kin file...
Determining Unique Individual IDs from KING Output...
Checking Provided Individual IDs
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 7.719 secs
...SNP Block 2 of 2 Completed - 6.375 secs
Performing Small Sample Correction...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 7.003 secs
...SNP Block 2 of 2 Completed - 6.591 secs
Performing Small Sample Correction...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Creating GDS file for Allele Frequency Estimates:
Estimating Allele Frequencies...
...SNP Block 1 of 2 Completed - 0.5313 secs
...SNP Block 2 of 2 Completed - 0.5469 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 6.578 secs
...SNP Block 2 of 2 Completed - 7.797 secs
Performing Small Sample Correction...
Partitioning Samples into Related and Unrelated Sets...
Unrelated Set: 97 Samples 
Related Set: 76 Samples
Running Analysis with 20000 SNPs - in 2 Block(s)
Computing Genetic Correlation Matrix for the Unrelated Set: Block 1 of 2 ...
Computing Genetic Correlation Matrix for the Unrelated Set: Block 2 of 2 ...
Performing PCA on the Unrelated Set...
Predicting PC Values for the Related Set: Block 1 of 2 ...
Predicting PC Values for the Related Set: Block 2 of 2 ...
Concatenating Results...
Running Analysis with 20000 SNPs - in 2 Block(s)
Running Analysis with 173 Samples - in 1 Block(s)
Using 2 PC(s) in pcMat to Calculate Adjusted Estimates
Using all 173 Samples to Estimate PC effects on Allele Frequencies
Creating GDS file for Allele Frequency Estimates:
Estimating Allele Frequencies...
...SNP Block 1 of 2 Completed - 0.8125 secs
...SNP Block 2 of 2 Completed - 0.7344 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 7.701 secs
...SNP Block 2 of 2 Completed - 6.379 secs
Performing Small Sample Correction...


RUNIT TEST PROTOCOL -- Thu Apr 12 00:24:52 2018 
*********************************************** 
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GENESIS RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 121.60    4.04  127.60

Example timings

GENESIS.Rcheck/examples_i386/GENESIS-Ex.timings

nameusersystemelapsed
admixMapMM8.690.709.51
assocTestMM12.47 0.8013.44
assocTestSeq0.890.011.53
assocTestSeqWindow2.110.032.14
fitNullMM11.58 0.5212.09
king2mat0.420.000.43
pcair0.910.121.03
pcairPartition0.060.000.06
pcrelate11.36 0.6111.97
plot.pcair1.090.091.19
varCompCI12.47 0.6413.10

GENESIS.Rcheck/examples_x64/GENESIS-Ex.timings

nameusersystemelapsed
admixMapMM 9.87 0.5910.98
assocTestMM12.06 0.7312.86
assocTestSeq0.970.001.50
assocTestSeqWindow2.470.002.47
fitNullMM16.92 0.8517.79
king2mat0.30.00.3
pcair0.730.060.80
pcairPartition0.090.000.09
pcrelate14.61 0.6315.23
plot.pcair1.690.041.74
varCompCI15.06 0.5215.58