BioC 3.5: CHECK report for spliceSites on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/spliceSites.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 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
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	0.732	0.004	0.736
addGeneAligns	0.072	0.008	0.079
addGenomeData-ExpressionSet	0.768	0.000	0.767
addGenomeData-gapSites	0.428	0.000	0.430
addHbond	0.120	0.000	0.123
addMaxEnt	0.160	0.000	0.162
alt_X_ranks	0.02	0.00	0.02
annGapSites-class	0.048	0.004	0.054
annotate-ExpressionSet	0.252	0.000	0.256
annotation	0.016	0.000	0.017
cRanges-class	0.044	0.004	0.048
caRanges-class	0.100	0.000	0.099
cdRanges-class	0.684	0.000	0.682
countByGeneName	0.268	0.000	0.267
dnaGapSites-class	0.192	0.012	0.205
dnaRanges	0.284	0.004	0.286
extractByGeneName	0.148	0.000	0.149
extractRange	0.032	0.000	0.032
gapSites-class	0.036	0.000	0.035
gapSites	0.072	0.000	0.074
getGapSites	0.036	0.000	0.036
hbond-class	0.024	0.004	0.027
keyProfiler-class	0.028	0.000	0.028
lrCodons	0.048	0.000	0.048
maxEnt-class	0.016	0.004	0.020
plotGeneAlignDepth	0.076	0.000	0.077
rangeByGeneName	0.036	0.000	0.035
readCuffGeneFpkm	0.044	0.000	0.044
readExpSet	0.056	0.004	0.057
readMergedBamGaps	0.084	0.000	0.084
readTabledBamGaps	0.144	0.000	0.142
seqlogo	0.112	0.004	0.115
silic_tryp	0.000	0.000	0.002
spliceSites-package	0.036	0.000	0.034
trim	0.02	0.00	0.02
truncateSeq	0.084	0.004	0.085
truncate_seq	0.000	0.000	0.001
trypsinCleave	0.068	0.000	0.068
uniqueJuncAnn	0.100	0.000	0.102
write.files	0.052	0.000	0.051
xCodons	0.044	0.000	0.043
xJunc	0.02	0.00	0.02
xJuncStrand	0.056	0.004	0.056

BioC 3.5: CHECK report for spliceSites on malbec2

Summary

Command output