BioC 3.5: CHECK report for spliceSites on toluca2

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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_1.23.5.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 r72187)
* 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 ‘1.23.5’
* 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	0.001	0.000	0.000
aaGapSites-class	0.949	0.008	1.104
addGeneAligns	0.134	0.017	0.168
addGenomeData-ExpressionSet	1.223	0.013	1.410
addGenomeData-gapSites	0.623	0.009	0.713
addHbond	0.161	0.005	0.186
addMaxEnt	0.489	0.004	0.559
alt_X_ranks	0.029	0.001	0.034
annGapSites-class	0.077	0.002	0.089
annotate-ExpressionSet	0.412	0.005	0.470
annotation	0.026	0.001	0.030
cRanges-class	0.077	0.002	0.090
caRanges-class	0.118	0.003	0.138
cdRanges-class	0.501	0.078	0.654
countByGeneName	0.482	0.003	0.559
dnaGapSites-class	0.312	0.006	0.358
dnaRanges	0.689	0.013	0.792
extractByGeneName	0.233	0.002	0.270
extractRange	0.056	0.002	0.063
gapSites-class	0.046	0.002	0.054
gapSites	0.105	0.003	0.121
getGapSites	0.048	0.002	0.056
hbond-class	0.031	0.000	0.034
keyProfiler-class	0.048	0.001	0.056
lrCodons	0.075	0.001	0.084
maxEnt-class	0.017	0.002	0.020
plotGeneAlignDepth	0.087	0.003	0.104
rangeByGeneName	0.053	0.001	0.057
readCuffGeneFpkm	0.060	0.002	0.076
readExpSet	0.073	0.001	0.084
readMergedBamGaps	0.137	0.001	0.154
readTabledBamGaps	0.217	0.002	0.245
seqlogo	0.133	0.008	0.160
silic_tryp	0.001	0.000	0.002
spliceSites-package	0.039	0.003	0.048
trim	0.029	0.001	0.034
truncateSeq	0.100	0.004	0.118
truncate_seq	0.002	0.000	0.002
trypsinCleave	0.098	0.003	0.113
uniqueJuncAnn	0.160	0.002	0.182
write.files	0.071	0.003	0.085
xCodons	0.059	0.001	0.068
xJunc	0.031	0.001	0.036
xJuncStrand	0.103	0.001	0.119

BioC 3.5: CHECK report for spliceSites on toluca2

Summary

Command output