Package: GENESIS

Version: 2.8.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GENESIS_2.8.1.tar.gz

StartedAt: 2018-04-11 23:46:08 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:50:55 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 286.4 seconds

RetCode: 0

Status:  OK

CheckDir: GENESIS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GENESIS_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GENESIS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
assocTestMM 12.832  0.044  12.896
varCompCI   11.160  0.020  11.190
pcrelate    11.000  0.028  11.034
fitNullMM   10.752  0.008  10.767
admixMapMM   8.012  0.284   8.402
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GENESIS.Rcheck/00check.log’
for details.

* installing *source* package ‘GENESIS’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GENESIS)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 - 5.956 secs
...SNP Block 2 of 2 Completed - 4.917 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 - 4.877 secs
...SNP Block 2 of 2 Completed - 5.422 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 - 0.4279 secs
...SNP Block 2 of 2 Completed - 0.7239 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 4.848 secs
...SNP Block 2 of 2 Completed - 5.4 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 - 0.7354 secs
...SNP Block 2 of 2 Completed - 0.4292 secs
Creating GDS file for PC-Relate Results:
Computing Relatedness Estimates...
...SNP Block 1 of 2 Completed - 6.029 secs
...SNP Block 2 of 2 Completed - 4.961 secs
Performing Small Sample Correction...


RUNIT TEST PROTOCOL -- Wed Apr 11 23:50:51 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 
 89.248   0.752  90.733 

name	user	system	elapsed
admixMapMM	8.012	0.284	8.402
assocTestMM	12.832	0.044	12.896
assocTestSeq	1.004	0.000	1.137
assocTestSeqWindow	2.360	0.008	2.371
fitNullMM	10.752	0.008	10.767
king2mat	0.252	0.000	0.252
pcair	0.548	0.000	0.547
pcairPartition	0.056	0.000	0.056
pcrelate	11.000	0.028	11.034
plot.pcair	0.660	0.012	0.675
varCompCI	11.16	0.02	11.19