BioC 3.5: CHECK report for VanillaICE on oaxaca

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VanillaICE_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.37.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘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 ... 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.

* installing *source* package ‘VanillaICE’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c rinit.c -o rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c viterbi.c -o viterbi.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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	4.221	0.092	4.469
CopyNumScanParams	0.003	0.000	0.004
EmissionParam-methods	0.015	0.001	0.016
FilterParam-class	0.005	0.000	0.005
HMM	0.920	0.048	0.969
HMMList-class	0.710	0.013	0.723
HmmParam	0.004	0.001	0.005
IO	0.006	0.000	0.006
IdiogramParams-class	0.291	0.005	0.331
SnpArrayExperiment-class	0.290	0.005	0.332
SnpExperiment	0.062	0.000	0.072
SnpGRanges	0.146	0.001	0.169
TransitionParam	0.002	0.000	0.002
cnvFilter	1.416	0.009	1.567
dropDuplicatedMapLocs	0.290	0.005	0.331
emissionParam	0.036	0.000	0.041
getExampleSnpExperiment	0.001	0.000	0.001
getHmmParams	0.019	0.000	0.021
hmm2	0.683	0.008	0.788
isHeterozygous	0.338	0.012	0.398
parseSourceFile	0.660	0.024	0.733
plotting	2.082	0.041	2.391
robust-statistics	0.001	0.000	0.001
snpArrayAssays	0.013	0.004	0.021
sourcePaths	0.009	0.000	0.011
sweepMode	0.272	0.005	0.316
threshold	0.001	0.000	0.001
viewports	0.019	0.001	0.022

BioC 3.5: CHECK report for VanillaICE on oaxaca

Summary

Command output