BioC 2.13: CHECK report for spliceSites on perceval

Package: spliceSites

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spliceSites_1.0.0.tar.gz

StartedAt: 2014-04-05 04:34:39 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:39:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 314.8 seconds

RetCode: 0

Status:  OK

CheckDir: spliceSites.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/spliceSites.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [33s/34s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c spliceSites.c -o spliceSites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.002	0.003	0.006
aaGapSites-class	0.770	0.046	0.844
addGeneAlignPart	0.122	0.008	0.137
addHbond	0.948	0.034	1.000
addMaxEnt	0.460	0.023	0.486
alt_X_ranks	0.038	0.007	0.046
annGapSites-class	0.138	0.016	0.153
annotate-ExpressionSet	0.250	0.016	0.268
annotation	0.080	0.011	0.093
cRanges-class	0.097	0.016	0.114
caRanges-class	0.180	0.014	0.196
cdRanges-class	1.652	0.290	1.980
countByGeneName	0.132	0.015	0.156
dnaGapSites-class	0.851	0.019	0.884
dnaRanges	0.377	0.027	0.414
extractByGeneName	0.307	0.022	0.331
extractRange	0.052	0.009	0.064
gapSites-class	0.089	0.015	0.138
gapSites	0.240	0.022	0.262
getGapSites	0.086	0.011	0.096
hbond-class	0.015	0.007	0.021
keyProfiler-class	0.042	0.012	0.053
lrCodons	0.062	0.014	0.076
maxEnt-class	0.034	0.013	0.047
rangeByGeneName	0.057	0.011	0.067
readCuffGeneFpkm	0.117	0.013	0.131
readExpSet	0.138	0.015	0.156
readMergedBamGaps	0.041	0.009	0.050
readTabledBamGaps	0.098	0.014	0.113
silic_tryp	0.010	0.003	0.014
spliceSites-package	0.103	0.018	0.124
trim	0.555	0.019	0.582
truncateSeq	0.129	0.019	0.149
truncate_seq	0.005	0.004	0.009
trypsinCleave	0.146	0.017	0.166
uniqueJuncAnn	0.185	0.017	0.208
write.files	0.119	0.014	0.133
xCodons	0.051	0.013	0.063
xJunc	0.056	0.010	0.066
xJuncStrand	0.050	0.011	0.061