BioC 3.0: CHECK report for VanillaICE on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.28.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/VanillaICE.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.28.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doMPI’ ‘doRedis’
* 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 ‘VanillaICE’ can be installed ... [23s/23s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg18’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘GenomicRanges:::.ShallowSimpleListAssays’
  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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [35s/35s]
 [35s/35s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘distance’ in package ‘VanillaICE’
Creating a generic function for ‘scale’ from package ‘base’ in package ‘VanillaICE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VanillaICE)

name	user	system	elapsed
ArrayViews-class	4.676	0.160	4.851
CopyNumScanParams	0.004	0.000	0.003
EmissionParam-methods	0.012	0.000	0.012
FilterParam-class	0.004	0.000	0.003
HMM	0.232	0.012	0.246
HMMList-class	0.857	0.004	0.860
HmmParam	0.008	0.000	0.005
IO	0.012	0.000	0.011
IdiogramParams-class	0.284	0.000	0.290
SnpArrayExperiment-class	0.044	0.000	0.046
SnpExperiment	0.024	0.000	0.021
SnpGRanges	0.028	0.000	0.030
TransitionParam	0.000	0.000	0.001
cnvFilter	0.888	0.004	0.892
constraints	0.000	0.000	0.001
dropDuplicatedMapLocs	0.108	0.000	0.107
emissionParam	0.004	0.000	0.005
getExampleSnpExperiment	0.000	0.004	0.001
getHmmParams	0.012	0.000	0.011
hmm2	0.504	0.000	0.505
icePlatforms	0.004	0.000	0.001
parseSourceFile	0.512	0.016	0.527
plotting	1.624	0.008	1.635
robust-statistics	0.000	0.000	0.001
snpArrayAssays	0.012	0.000	0.010
sourcePaths	0.012	0.000	0.011
sweepMode	0.236	0.000	0.235
threshold	0.000	0.000	0.001
viewports	0.000	0.000	0.002

BioC 3.0: CHECK report for VanillaICE on zin1

Summary

Command output