BioC 3.6: CHECK report for spliceSites on veracruz1

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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_1.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.25.0’
* 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   -fPIC  -Wall -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-3.6-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	0.001
aaGapSites-class	0.741	0.016	0.782
addGeneAligns	0.104	0.009	0.115
addGenomeData-ExpressionSet	0.973	0.006	1.006
addGenomeData-gapSites	0.503	0.007	0.529
addHbond	0.139	0.006	0.153
addMaxEnt	0.175	0.003	0.179
alt_X_ranks	0.023	0.003	0.025
annGapSites-class	0.074	0.003	0.079
annotate-ExpressionSet	0.273	0.002	0.288
annotation	0.021	0.001	0.022
cRanges-class	0.058	0.002	0.061
caRanges-class	0.111	0.003	0.116
cdRanges-class	0.694	0.071	0.787
countByGeneName	0.370	0.012	0.393
dnaGapSites-class	0.229	0.017	0.255
dnaRanges	0.338	0.013	0.368
extractByGeneName	0.187	0.003	0.196
extractRange	0.045	0.001	0.051
gapSites-class	0.041	0.003	0.044
gapSites	0.084	0.002	0.090
getGapSites	0.040	0.001	0.042
hbond-class	0.022	0.001	0.023
keyProfiler-class	0.041	0.001	0.042
lrCodons	0.057	0.000	0.058
maxEnt-class	0.016	0.001	0.017
plotGeneAlignDepth	0.086	0.012	0.104
rangeByGeneName	0.044	0.001	0.046
readCuffGeneFpkm	0.053	0.001	0.055
readExpSet	0.067	0.001	0.071
readMergedBamGaps	0.092	0.001	0.093
readTabledBamGaps	0.176	0.007	0.187
seqlogo	0.125	0.010	0.142
silic_tryp	0.001	0.000	0.002
spliceSites-package	0.037	0.003	0.041
trim	0.027	0.002	0.030
truncateSeq	0.084	0.002	0.090
truncate_seq	0.001	0.001	0.009
trypsinCleave	0.091	0.003	0.096
uniqueJuncAnn	0.131	0.002	0.136
write.files	0.062	0.001	0.063
xCodons	0.048	0.001	0.049
xJunc	0.026	0.001	0.027
xJuncStrand	0.072	0.001	0.072

BioC 3.6: CHECK report for spliceSites on veracruz1

Summary

Command output