Package: spliceSites

Version: 1.31.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings spliceSites_1.31.0.tar.gz

StartedAt: 2019-03-18 04:54:16 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 04:56:45 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 148.3 seconds

RetCode: 0

Status:  OK

CheckDir: spliceSites.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings spliceSites_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/spliceSites.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* 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 ‘1.31.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.gapSites merge.gapSites
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL spliceSites
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘spliceSites’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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	0.709	0.004	1.014
addGeneAligns	0.079	0.000	0.253
addGenomeData-ExpressionSet	0.456	0.052	0.530
addGenomeData-gapSites	0.470	0.004	0.475
addHbond	0.122	0.004	0.223
addMaxEnt	0.259	0.000	0.260
alt_X_ranks	0.020	0.000	0.021
annGapSites-class	0.087	0.004	0.091
annotate-ExpressionSet	0.163	0.000	0.162
annotation	0.026	0.000	0.026
cRanges-class	0.047	0.000	0.047
caRanges-class	0.103	0.003	0.106
cdRanges-class	0.786	0.020	0.807
countByGeneName	0.054	0.000	0.053
dnaGapSites-class	0.194	0.000	0.193
dnaRanges	0.341	0.000	0.343
extractByGeneName	0.201	0.000	0.201
extractRange	0.018	0.000	0.018
gapSites-class	0.034	0.004	0.038
gapSites	0.064	0.004	0.069
getGapSites	0.041	0.004	0.045
hbond-class	0.008	0.000	0.008
keyProfiler-class	0.011	0.000	0.061
lrCodons	0.045	0.000	0.045
maxEnt-class	0.019	0.000	0.019
plotGeneAlignDepth	0.077	0.000	0.077
rangeByGeneName	0.03	0.00	0.03
readCuffGeneFpkm	0.050	0.000	0.098
readExpSet	0.088	0.004	0.092
readMergedBamGaps	0.029	0.000	0.029
readTabledBamGaps	0.149	0.000	0.149
seqlogo	0.175	0.004	0.179
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.051	0.000	0.051
trim	0.028	0.004	0.032
truncateSeq	0.078	0.000	0.079
truncate_seq	0.003	0.000	0.002
trypsinCleave	0.086	0.000	0.087
uniqueJuncAnn	0.119	0.000	0.118
write.files	0.070	0.004	0.074
xCodons	0.034	0.000	0.034
xJunc	0.032	0.000	0.033
xJuncStrand	0.032	0.000	0.033