Package: spliceSites

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.26.0.tar.gz

StartedAt: 2018-04-12 09:54:33 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 09:57:05 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 152.4 seconds

RetCode: 0

Status:  OK

CheckDir: spliceSites.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.26.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spliceSites.c -o spliceSites.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-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	0.538	0.025	0.569
addGeneAligns	0.093	0.002	0.095
addGenomeData-ExpressionSet	0.885	0.006	0.899
addGenomeData-gapSites	0.479	0.006	0.488
addHbond	0.317	0.005	0.330
addMaxEnt	0.159	0.012	0.173
alt_X_ranks	0.023	0.003	0.026
annGapSites-class	0.067	0.011	0.082
annotate-ExpressionSet	0.293	0.005	0.315
annotation	0.018	0.001	0.018
cRanges-class	0.056	0.003	0.062
caRanges-class	0.107	0.003	0.110
cdRanges-class	0.370	0.066	0.454
countByGeneName	0.344	0.006	0.354
dnaGapSites-class	0.199	0.003	0.204
dnaRanges	0.292	0.014	0.314
extractByGeneName	0.186	0.003	0.193
extractRange	0.042	0.001	0.044
gapSites-class	0.037	0.002	0.040
gapSites	0.319	0.004	0.324
getGapSites	0.036	0.001	0.038
hbond-class	0.023	0.000	0.026
keyProfiler-class	0.035	0.001	0.035
lrCodons	0.050	0.001	0.051
maxEnt-class	0.015	0.001	0.016
plotGeneAlignDepth	0.068	0.003	0.077
rangeByGeneName	0.039	0.001	0.041
readCuffGeneFpkm	0.045	0.002	0.047
readExpSet	0.064	0.001	0.065
readMergedBamGaps	0.097	0.003	0.103
readTabledBamGaps	0.165	0.002	0.172
seqlogo	0.102	0.007	0.112
silic_tryp	0.001	0.000	0.002
spliceSites-package	0.037	0.003	0.042
trim	0.038	0.001	0.039
truncateSeq	0.081	0.002	0.087
truncate_seq	0.001	0.000	0.002
trypsinCleave	0.077	0.001	0.078
uniqueJuncAnn	0.115	0.001	0.118
write.files	0.046	0.000	0.046
xCodons	0.050	0.001	0.050
xJunc	0.025	0.001	0.027
xJuncStrand	0.069	0.001	0.073