Package: spliceSites

Version: 1.28.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings spliceSites_1.28.0.tar.gz

StartedAt: 2018-10-16 03:56:30 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:58:07 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 97.5 seconds

RetCode: 0

Status:  OK

CheckDir: spliceSites.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings spliceSites_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/spliceSites.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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 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 ... NOTE
Note: information on .o files is not available
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL spliceSites
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘spliceSites’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/spliceSites/libs
** R
** inst
** byte-compile and prepare 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	0.504	0.004	0.533
addGeneAligns	0.048	0.000	0.047
addGenomeData-ExpressionSet	0.384	0.052	0.447
addGenomeData-gapSites	0.388	0.036	0.424
addHbond	0.124	0.004	0.126
addMaxEnt	0.172	0.000	0.172
alt_X_ranks	0.016	0.000	0.014
annGapSites-class	0.052	0.004	0.057
annotate-ExpressionSet	0.104	0.000	0.107
annotation	0.02	0.00	0.02
cRanges-class	0.032	0.000	0.033
caRanges-class	0.064	0.000	0.064
cdRanges-class	0.656	0.000	0.656
countByGeneName	0.052	0.000	0.051
dnaGapSites-class	0.188	0.000	0.187
dnaRanges	0.216	0.004	0.220
extractByGeneName	0.140	0.000	0.138
extractRange	0.020	0.000	0.018
gapSites-class	0.036	0.000	0.037
gapSites	0.08	0.00	0.08
getGapSites	0.040	0.000	0.036
hbond-class	0.008	0.000	0.007
keyProfiler-class	0.012	0.000	0.013
lrCodons	0.048	0.000	0.046
maxEnt-class	0.016	0.004	0.020
plotGeneAlignDepth	0.072	0.004	0.074
rangeByGeneName	0.036	0.000	0.034
readCuffGeneFpkm	0.044	0.004	0.064
readExpSet	0.052	0.000	0.053
readMergedBamGaps	0.02	0.00	0.02
readTabledBamGaps	0.080	0.008	0.086
seqlogo	0.104	0.000	0.104
silic_tryp	0.000	0.000	0.002
spliceSites-package	0.032	0.000	0.033
trim	0.020	0.000	0.021
truncateSeq	0.056	0.004	0.059
truncate_seq	0.000	0.000	0.001
trypsinCleave	0.068	0.000	0.068
uniqueJuncAnn	0.076	0.000	0.077
write.files	0.056	0.000	0.057
xCodons	0.028	0.000	0.027
xJunc	0.02	0.00	0.02
xJuncStrand	0.02	0.00	0.02