BioC 3.4: CHECK report for VanillaICE on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/VanillaICE.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘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 ... 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
Namespace in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘SummarizedExperiment:::.ShallowSimpleListAssays0’
  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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘distance’ 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	2.796	0.116	2.935
CopyNumScanParams	0.004	0.000	0.003
EmissionParam-methods	0.012	0.004	0.014
FilterParam-class	0.000	0.004	0.004
HMM	0.256	0.004	0.263
HMMList-class	0.456	0.004	0.460
HmmParam	0.008	0.000	0.005
IO	0.012	0.000	0.011
IdiogramParams-class	0.220	0.004	0.223
SnpArrayExperiment-class	0.076	0.000	0.076
SnpExperiment	0.032	0.000	0.032
SnpGRanges	0.024	0.000	0.024
TransitionParam	0.004	0.000	0.001
cnvFilter	0.620	0.000	0.622
dropDuplicatedMapLocs	0.096	0.000	0.094
emissionParam	0.004	0.000	0.004
getExampleSnpExperiment	0	0	0
getHmmParams	0.008	0.000	0.007
hmm2	0.448	0.004	0.455
isHeterozygous	0.376	0.000	0.382
parseSourceFile	0.436	0.000	0.435
plotting	1.604	0.012	1.616
robust-statistics	0.000	0.000	0.001
snpArrayAssays	0.008	0.000	0.010
sourcePaths	0.004	0.000	0.007
sweepMode	0.156	0.000	0.157
threshold	0	0	0
viewports	0.004	0.000	0.001

BioC 3.4: CHECK report for VanillaICE on malbec1

Summary

Command output