BioC 3.2: 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_1.8.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/spliceSites.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.8.3’
* 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 ... [16s/16s] 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 ... [11s/11s] 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-3.2-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	0.000	0.000	0.001
aaGapSites-class	0.213	0.003	0.243
addGeneAligns	0.046	0.001	0.047
addHbond	0.478	0.005	0.482
addMaxEnt	0.292	0.022	0.314
alt_X_ranks	0.018	0.001	0.018
annGapSites-class	0.042	0.002	0.044
annotate-ExpressionSet	0.156	0.002	0.158
annotation	0.026	0.001	0.027
cRanges-class	0.044	0.002	0.047
caRanges-class	0.317	0.007	0.323
cdRanges-class	0.581	0.081	0.663
countByGeneName	0.074	0.002	0.075
dnaGapSites-class	0.250	0.005	0.255
dnaRanges	0.248	0.012	0.264
extractByGeneName	0.229	0.004	0.233
extractRange	0.029	0.002	0.032
gapSites-class	0.054	0.003	0.057
gapSites	0.114	0.001	0.115
getGapSites	0.052	0.001	0.054
hbond-class	0.009	0.002	0.010
keyProfiler-class	0.023	0.000	0.023
lrCodons	0.045	0.001	0.046
maxEnt-class	0.023	0.002	0.025
plotGeneAlignDepth	0.091	0.004	0.095
rangeByGeneName	0.034	0.001	0.035
readCuffGeneFpkm	0.078	0.002	0.080
readExpSet	0.093	0.002	0.094
readMergedBamGaps	0.020	0.001	0.021
readTabledBamGaps	0.057	0.001	0.059
seqlogo	0.149	0.007	0.157
silic_tryp	0.001	0.000	0.002
spliceSites-package	0.045	0.002	0.048
trim	0.030	0.002	0.031
truncateSeq	0.071	0.002	0.073
truncate_seq	0.001	0.001	0.002
trypsinCleave	0.090	0.003	0.093
uniqueJuncAnn	0.113	0.001	0.115
write.files	0.072	0.001	0.073
xCodons	0.024	0.001	0.025
xJunc	0.030	0.001	0.030
xJuncStrand	0.030	0.001	0.031

BioC 3.2: CHECK report for spliceSites on oaxaca

Summary

Command output