BioC 2.13: CHECK report for spliceSites on zin1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/spliceSites.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘1.0.0’
* 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 ... [19s/19s] 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 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 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 ... [14s/14s] 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

* installing *source* package ‘spliceSites’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -std=gnu99 -shared -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘rbamtools::coerce’ when loading ‘spliceSites’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘rbamtools::coerce’ when loading ‘spliceSites’
* DONE (spliceSites)

name	user	system	elapsed
SpliceCountSet-class	0.004	0.000	0.001
aaGapSites-class	0.472	0.016	0.488
addGeneAlignPart	0.088	0.004	0.093
addHbond	0.508	0.008	0.514
addMaxEnt	0.308	0.004	0.314
alt_X_ranks	0.020	0.000	0.021
annGapSites-class	0.088	0.000	0.086
annotate-ExpressionSet	0.156	0.004	0.161
annotation	0.036	0.008	0.046
cRanges-class	0.052	0.004	0.056
caRanges-class	0.108	0.000	0.108
cdRanges-class	0.952	0.008	0.960
countByGeneName	0.088	0.004	0.095
dnaGapSites-class	0.284	0.008	0.293
dnaRanges	0.308	0.004	0.311
extractByGeneName	0.224	0.004	0.228
extractRange	0.032	0.000	0.035
gapSites-class	0.060	0.000	0.059
gapSites	0.144	0.000	0.146
getGapSites	0.056	0.004	0.059
hbond-class	0.016	0.000	0.013
keyProfiler-class	0.032	0.000	0.029
lrCodons	0.268	0.004	0.273
maxEnt-class	0.020	0.004	0.025
rangeByGeneName	0.040	0.004	0.041
readCuffGeneFpkm	0.072	0.000	0.069
readExpSet	0.112	0.000	0.112
readMergedBamGaps	0.028	0.004	0.031
readTabledBamGaps	0.068	0.000	0.069
silic_tryp	0.004	0.000	0.004
spliceSites-package	0.072	0.004	0.102
trim	0.036	0.004	0.040
truncateSeq	0.096	0.000	0.096
truncate_seq	0.004	0.000	0.004
trypsinCleave	0.104	0.000	0.107
uniqueJuncAnn	0.128	0.004	0.131
write.files	0.080	0.008	0.088
xCodons	0.040	0.000	0.042
xJunc	0.036	0.000	0.037
xJuncStrand	0.032	0.000	0.033

BioC 2.13: CHECK report for spliceSites on zin1

Summary

Command output