BioC 3.2: CHECK report for spliceSites on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.8.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/spliceSites.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.8.3’
* 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 ... [12s/12s] 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 ... [9s/9s] 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 -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	0	0
aaGapSites-class	0.192	0.004	0.212
addGeneAligns	0.037	0.000	0.039
addHbond	0.411	0.004	0.452
addMaxEnt	0.233	0.015	0.256
alt_X_ranks	0.017	0.000	0.017
annGapSites-class	0.043	0.000	0.042
annotate-ExpressionSet	0.360	0.000	0.373
annotation	0.022	0.000	0.022
cRanges-class	0.042	0.000	0.042
caRanges-class	0.081	0.000	0.081
cdRanges-class	0.382	0.008	0.400
countByGeneName	0.064	0.000	0.064
dnaGapSites-class	0.195	0.000	0.195
dnaRanges	0.482	0.000	0.481
extractByGeneName	0.178	0.000	0.178
extractRange	0.023	0.000	0.023
gapSites-class	0.043	0.000	0.044
gapSites	0.109	0.000	0.108
getGapSites	0.044	0.001	0.044
hbond-class	0.008	0.000	0.009
keyProfiler-class	0.015	0.000	0.016
lrCodons	0.031	0.000	0.030
maxEnt-class	0.02	0.00	0.02
plotGeneAlignDepth	0.083	0.000	0.084
rangeByGeneName	0.021	0.000	0.025
readCuffGeneFpkm	0.061	0.004	0.064
readExpSet	0.071	0.000	0.070
readMergedBamGaps	0.024	0.000	0.023
readTabledBamGaps	0.052	0.000	0.052
seqlogo	0.151	0.000	0.151
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.046	0.001	0.046
trim	0.028	0.000	0.029
truncateSeq	0.069	0.003	0.073
truncate_seq	0.002	0.000	0.002
trypsinCleave	0.080	0.000	0.081
uniqueJuncAnn	0.102	0.000	0.102
write.files	0.074	0.000	0.075
xCodons	0.026	0.004	0.030
xJunc	0.027	0.000	0.028
xJuncStrand	0.027	0.000	0.026

BioC 3.2: CHECK report for spliceSites on zin1

Summary

Command output