BioC 3.5: CHECK report for spliceSites on veracruz2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/spliceSites.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.24.0’
* 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-3.5-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	0.000	0.000	0.001
aaGapSites-class	0.884	0.008	0.917
addGeneAligns	0.108	0.016	0.125
addGenomeData-ExpressionSet	1.010	0.017	1.052
addGenomeData-gapSites	0.555	0.011	0.574
addHbond	0.148	0.005	0.159
addMaxEnt	0.203	0.004	0.210
alt_X_ranks	0.030	0.001	0.032
annGapSites-class	0.072	0.003	0.075
annotate-ExpressionSet	0.339	0.006	0.364
annotation	0.021	0.000	0.022
cRanges-class	0.071	0.003	0.078
caRanges-class	0.143	0.004	0.150
cdRanges-class	1.019	0.080	1.130
countByGeneName	0.326	0.004	0.354
dnaGapSites-class	0.250	0.003	0.261
dnaRanges	0.344	0.012	0.375
extractByGeneName	0.206	0.004	0.216
extractRange	0.045	0.001	0.049
gapSites-class	0.042	0.002	0.046
gapSites	0.088	0.004	0.093
getGapSites	0.044	0.001	0.047
hbond-class	0.023	0.001	0.024
keyProfiler-class	0.040	0.001	0.041
lrCodons	0.061	0.001	0.063
maxEnt-class	0.016	0.001	0.018
plotGeneAlignDepth	0.079	0.004	0.084
rangeByGeneName	0.044	0.001	0.046
readCuffGeneFpkm	0.047	0.001	0.049
readExpSet	0.064	0.002	0.067
readMergedBamGaps	0.113	0.003	0.118
readTabledBamGaps	0.179	0.002	0.190
seqlogo	0.129	0.006	0.140
silic_tryp	0.001	0.000	0.003
spliceSites-package	0.037	0.003	0.043
trim	0.045	0.002	0.048
truncateSeq	0.086	0.002	0.091
truncate_seq	0.001	0.001	0.002
trypsinCleave	0.086	0.001	0.089
uniqueJuncAnn	0.126	0.001	0.134
write.files	0.067	0.002	0.071
xCodons	0.050	0.001	0.051
xJunc	0.027	0.001	0.028
xJuncStrand	0.081	0.002	0.086

BioC 3.5: CHECK report for spliceSites on veracruz2

Summary

Command output