Package: spliceSites

Version: 1.26.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.26.0.tar.gz

StartedAt: 2018-04-12 03:06:03 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:08:04 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 120.6 seconds

RetCode: 0

Status:  OK

CheckDir: spliceSites.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/spliceSites.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.26.0’
* 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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.436	0.020	0.454
addGeneAligns	0.080	0.000	0.078
addGenomeData-ExpressionSet	0.796	0.000	0.796
addGenomeData-gapSites	0.724	0.004	0.731
addHbond	0.128	0.004	0.132
addMaxEnt	0.168	0.004	0.172
alt_X_ranks	0.02	0.00	0.02
annGapSites-class	0.056	0.000	0.055
annotate-ExpressionSet	0.244	0.012	0.255
annotation	0.016	0.000	0.017
cRanges-class	0.044	0.004	0.050
caRanges-class	0.112	0.000	0.110
cdRanges-class	0.648	0.000	0.649
countByGeneName	0.288	0.000	0.287
dnaGapSites-class	0.196	0.000	0.195
dnaRanges	0.296	0.000	0.293
extractByGeneName	0.164	0.000	0.164
extractRange	0.036	0.000	0.036
gapSites-class	0.036	0.000	0.038
gapSites	0.076	0.004	0.079
getGapSites	0.040	0.000	0.042
hbond-class	0.020	0.000	0.019
keyProfiler-class	0.032	0.000	0.029
lrCodons	0.044	0.000	0.045
maxEnt-class	0.02	0.00	0.02
plotGeneAlignDepth	0.072	0.004	0.079
rangeByGeneName	0.032	0.000	0.032
readCuffGeneFpkm	0.040	0.000	0.041
readExpSet	0.052	0.004	0.053
readMergedBamGaps	0.076	0.000	0.077
readTabledBamGaps	0.132	0.000	0.131
seqlogo	0.108	0.004	0.112
silic_tryp	0.004	0.000	0.001
spliceSites-package	0.036	0.000	0.035
trim	0.032	0.000	0.035
truncateSeq	0.084	0.000	0.085
truncate_seq	0.000	0.000	0.001
trypsinCleave	0.072	0.000	0.073
uniqueJuncAnn	0.104	0.000	0.104
write.files	0.060	0.000	0.058
xCodons	0.048	0.000	0.046
xJunc	0.020	0.000	0.022
xJuncStrand	0.060	0.000	0.059