Package: spliceSites

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spliceSites_1.31.0.tar.gz

StartedAt: 2019-04-08 04:01:56 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 04:04:34 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 157.1 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 --install=check:spliceSites.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spliceSites_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/spliceSites.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.31.0’
* 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 sizes of PDF files under ‘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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL spliceSites
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/3.6/Resources/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	0.599	0.005	0.611
addGeneAligns	0.067	0.002	0.069
addGenomeData-ExpressionSet	0.608	0.075	0.693
addGenomeData-gapSites	0.605	0.057	0.671
addHbond	0.167	0.007	0.173
addMaxEnt	0.207	0.005	0.212
alt_X_ranks	0.016	0.000	0.017
annGapSites-class	0.090	0.003	0.094
annotate-ExpressionSet	0.134	0.004	0.137
annotation	0.022	0.001	0.024
cRanges-class	0.045	0.004	0.049
caRanges-class	0.094	0.004	0.098
cdRanges-class	0.813	0.123	0.944
countByGeneName	0.086	0.003	0.090
dnaGapSites-class	0.292	0.008	0.302
dnaRanges	0.319	0.017	0.341
extractByGeneName	0.216	0.003	0.222
extractRange	0.023	0.001	0.026
gapSites-class	0.038	0.002	0.041
gapSites	0.104	0.005	0.110
getGapSites	0.048	0.002	0.050
hbond-class	0.010	0.002	0.013
keyProfiler-class	0.020	0.000	0.021
lrCodons	0.074	0.001	0.076
maxEnt-class	0.020	0.002	0.022
plotGeneAlignDepth	0.091	0.005	0.099
rangeByGeneName	0.059	0.002	0.062
readCuffGeneFpkm	0.064	0.005	0.072
readExpSet	0.086	0.005	0.092
readMergedBamGaps	0.026	0.002	0.029
readTabledBamGaps	0.154	0.007	0.164
seqlogo	0.153	0.017	0.173
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.046	0.004	0.051
trim	0.029	0.002	0.032
truncateSeq	0.078	0.004	0.082
truncate_seq	0.003	0.000	0.003
trypsinCleave	0.085	0.005	0.091
uniqueJuncAnn	0.113	0.003	0.118
write.files	0.075	0.004	0.080
xCodons	0.029	0.003	0.034
xJunc	0.026	0.002	0.027
xJuncStrand	0.035	0.002	0.036