BioC 3.5: CHECK report for spliceSites on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.23.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/spliceSites.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 ‘spliceSites/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spliceSites’ version ‘1.23.3’
* 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 ‘spliceSites’ 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 ... OK
* 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 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 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: OK

* installing *source* package ‘spliceSites’ ...
** 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 spliceSites.c -o spliceSites.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 spliceSites.so spliceSites.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spliceSites)

name	user	system	elapsed
SpliceCountSet-class	0	0	0
aaGapSites-class	0.653	0.010	0.690
addGeneAligns	0.106	0.012	0.118
addGenomeData-ExpressionSet	1.021	0.013	1.034
addGenomeData-gapSites	0.541	0.009	0.550
addHbond	0.135	0.004	0.140
addMaxEnt	0.429	0.003	0.432
alt_X_ranks	0.026	0.001	0.026
annGapSites-class	0.059	0.002	0.061
annotate-ExpressionSet	0.383	0.003	0.386
annotation	0.019	0.001	0.020
cRanges-class	0.078	0.002	0.080
caRanges-class	0.130	0.003	0.133
cdRanges-class	0.740	0.072	0.813
countByGeneName	0.485	0.004	0.489
dnaGapSites-class	0.349	0.004	0.354
dnaRanges	0.388	0.012	0.414
extractByGeneName	0.179	0.006	0.185
extractRange	0.054	0.001	0.055
gapSites-class	0.044	0.002	0.045
gapSites	0.087	0.004	0.091
getGapSites	0.055	0.002	0.057
hbond-class	0.028	0.000	0.029
keyProfiler-class	0.030	0.001	0.031
lrCodons	0.068	0.000	0.068
maxEnt-class	0.018	0.002	0.018
plotGeneAlignDepth	0.084	0.003	0.088
rangeByGeneName	0.059	0.001	0.060
readCuffGeneFpkm	0.040	0.001	0.042
readExpSet	0.053	0.001	0.054
readMergedBamGaps	0.114	0.002	0.115
readTabledBamGaps	0.159	0.001	0.161
seqlogo	0.113	0.009	0.122
silic_tryp	0.001	0.000	0.002
spliceSites-package	0.030	0.002	0.032
trim	0.020	0.001	0.021
truncateSeq	0.110	0.002	0.113
truncate_seq	0.002	0.000	0.002
trypsinCleave	0.113	0.001	0.115
uniqueJuncAnn	0.108	0.001	0.109
write.files	0.058	0.000	0.058
xCodons	0.057	0.002	0.060
xJunc	0.032	0.001	0.032
xJuncStrand	0.121	0.003	0.125

BioC 3.5: CHECK report for spliceSites on oaxaca

Summary

Command output