BioC 3.5: CHECK report for spliceSites on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/spliceSites.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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	0.000	0.000	0.001
aaGapSites-class	0.736	0.008	0.758
addGeneAligns	0.072	0.008	0.078
addGenomeData-ExpressionSet	0.796	0.000	0.795
addGenomeData-gapSites	0.432	0.008	0.438
addHbond	0.124	0.000	0.125
addMaxEnt	0.172	0.000	0.170
alt_X_ranks	0.020	0.000	0.021
annGapSites-class	0.056	0.000	0.054
annotate-ExpressionSet	0.256	0.000	0.255
annotation	0.016	0.000	0.016
cRanges-class	0.052	0.000	0.050
caRanges-class	0.108	0.000	0.107
cdRanges-class	0.688	0.004	0.695
countByGeneName	0.280	0.000	0.278
dnaGapSites-class	0.200	0.000	0.198
dnaRanges	0.300	0.004	0.302
extractByGeneName	0.16	0.00	0.16
extractRange	0.036	0.000	0.034
gapSites-class	0.036	0.000	0.037
gapSites	0.120	0.004	0.122
getGapSites	0.068	0.000	0.065
hbond-class	0.032	0.000	0.033
keyProfiler-class	0.048	0.000	0.050
lrCodons	0.080	0.000	0.079
maxEnt-class	0.024	0.000	0.025
plotGeneAlignDepth	0.116	0.000	0.116
rangeByGeneName	0.060	0.000	0.059
readCuffGeneFpkm	0.068	0.000	0.065
readExpSet	0.052	0.000	0.054
readMergedBamGaps	0.084	0.000	0.083
readTabledBamGaps	0.128	0.000	0.129
seqlogo	0.112	0.000	0.109
silic_tryp	0.000	0.000	0.002
spliceSites-package	0.032	0.000	0.034
trim	0.032	0.004	0.033
truncateSeq	0.084	0.000	0.086
truncate_seq	0.004	0.000	0.002
trypsinCleave	0.072	0.000	0.073
uniqueJuncAnn	0.104	0.000	0.105
write.files	0.048	0.004	0.054
xCodons	0.044	0.000	0.044
xJunc	0.020	0.000	0.019
xJuncStrand	0.056	0.000	0.058

BioC 3.5: CHECK report for spliceSites on malbec2

Summary

Command output