Package: spliceSites

Version: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2018-10-17 00:13:33 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:16:06 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 153.0 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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/spliceSites.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-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/3.5/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/3.5/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	0.001	0.000	0.001
aaGapSites-class	0.573	0.006	0.585
addGeneAligns	0.075	0.004	0.079
addGenomeData-ExpressionSet	0.602	0.083	0.699
addGenomeData-gapSites	0.550	0.041	0.601
addHbond	0.170	0.005	0.178
addMaxEnt	0.215	0.005	0.222
alt_X_ranks	0.022	0.001	0.024
annGapSites-class	0.082	0.003	0.089
annotate-ExpressionSet	0.142	0.003	0.148
annotation	0.028	0.001	0.028
cRanges-class	0.052	0.004	0.056
caRanges-class	0.099	0.004	0.107
cdRanges-class	0.782	0.120	0.919
countByGeneName	0.078	0.002	0.083
dnaGapSites-class	0.284	0.004	0.294
dnaRanges	0.309	0.014	0.333
extractByGeneName	0.208	0.002	0.214
extractRange	0.024	0.001	0.026
gapSites-class	0.060	0.004	0.065
gapSites	0.100	0.004	0.106
getGapSites	0.050	0.002	0.054
hbond-class	0.010	0.002	0.013
keyProfiler-class	0.024	0.000	0.026
lrCodons	0.086	0.001	0.088
maxEnt-class	0.023	0.003	0.027
plotGeneAlignDepth	0.095	0.005	0.101
rangeByGeneName	0.047	0.002	0.051
readCuffGeneFpkm	0.071	0.006	0.080
readExpSet	0.084	0.002	0.087
readMergedBamGaps	0.026	0.001	0.028
readTabledBamGaps	0.121	0.002	0.126
seqlogo	0.127	0.008	0.143
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.050	0.004	0.055
trim	0.032	0.002	0.035
truncateSeq	0.070	0.003	0.075
truncate_seq	0.002	0.000	0.002
trypsinCleave	0.094	0.005	0.105
uniqueJuncAnn	0.113	0.001	0.121
write.files	0.079	0.001	0.081
xCodons	0.032	0.003	0.036
xJunc	0.028	0.000	0.029
xJuncStrand	0.032	0.001	0.033