BioC 3.3: CHECK report for GENESIS on zin2

Package: GENESIS

Version: 2.2.7

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GENESIS_2.2.7.tar.gz

StartedAt: 2016-10-13 02:24:16 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:29:51 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 335.2 seconds

RetCode: 0

Status:  OK

CheckDir: GENESIS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GENESIS_2.2.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GENESIS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.2.7’
* 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 15.784  0.391  16.410
pcrelate    11.156  0.248  11.539
varCompCI   11.127  0.136  11.300
fitNullMM   11.058  0.143  11.372
* 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-3.3-bioc/meat/GENESIS.Rcheck/00check.log’
for details.

* installing *source* package ‘GENESIS’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "SeqVarTools" for requests: variantData
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "SeqVarTools" for requests: variantData
* DONE (GENESIS)

name	user	system	elapsed
assocTestMM	15.784	0.391	16.410
assocTestSeq	0.640	0.008	0.688
assocTestSeqWindow	1.124	0.056	1.186
fitNullMM	11.058	0.143	11.372
king2mat	0.329	0.004	0.341
pcair	1.479	0.008	1.581
pcairPartition	0.079	0.000	0.079
pcrelate	11.156	0.248	11.539
plot.pcair	1.199	0.000	1.208
varCompCI	11.127	0.136	11.300