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CHECK report for GENESIS on malbec1

This page was generated on 2018-04-12 13:13:23 -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: /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

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

GENESIS.Rcheck/00install.out

* 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)

Tests output

GENESIS.Rcheck/tests/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-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 

Example timings

GENESIS.Rcheck/GENESIS-Ex.timings

nameusersystemelapsed
admixMapMM8.0120.2848.402
assocTestMM12.832 0.04412.896
assocTestSeq1.0040.0001.137
assocTestSeqWindow2.3600.0082.371
fitNullMM10.752 0.00810.767
king2mat0.2520.0000.252
pcair0.5480.0000.547
pcairPartition0.0560.0000.056
pcrelate11.000 0.02811.034
plot.pcair0.6600.0120.675
varCompCI11.16 0.0211.19