Package: spliceSites

Version: 1.30.0

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_1.30.0.tar.gz

StartedAt: 2019-03-18 03:03:36 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 03:06:07 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 151.5 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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/spliceSites.Rcheck’
* using R version 3.5.2 Patched (2018-12-20 r75875)
* 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 ‘1.30.0’
* 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-3.8-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	0.000	0.000	0.001
aaGapSites-class	0.614	0.006	0.636
addGeneAligns	0.071	0.004	0.075
addGenomeData-ExpressionSet	0.615	0.084	0.706
addGenomeData-gapSites	0.683	0.052	0.756
addHbond	0.192	0.007	0.203
addMaxEnt	0.235	0.006	0.244
alt_X_ranks	0.014	0.000	0.014
annGapSites-class	0.089	0.004	0.092
annotate-ExpressionSet	0.151	0.003	0.154
annotation	0.017	0.000	0.017
cRanges-class	0.034	0.002	0.037
caRanges-class	0.077	0.004	0.082
cdRanges-class	0.841	0.126	0.976
countByGeneName	0.091	0.002	0.093
dnaGapSites-class	0.347	0.005	0.357
dnaRanges	0.345	0.018	0.378
extractByGeneName	0.232	0.002	0.242
extractRange	0.025	0.001	0.027
gapSites-class	0.055	0.003	0.058
gapSites	0.094	0.004	0.100
getGapSites	0.043	0.001	0.045
hbond-class	0.010	0.002	0.013
keyProfiler-class	0.020	0.000	0.019
lrCodons	0.071	0.001	0.072
maxEnt-class	0.020	0.003	0.023
plotGeneAlignDepth	0.102	0.007	0.110
rangeByGeneName	0.061	0.002	0.067
readCuffGeneFpkm	0.069	0.006	0.076
readExpSet	0.076	0.002	0.079
readMergedBamGaps	0.024	0.001	0.025
readTabledBamGaps	0.143	0.003	0.148
seqlogo	0.142	0.008	0.151
silic_tryp	0.001	0.000	0.001
spliceSites-package	0.046	0.003	0.049
trim	0.037	0.002	0.039
truncateSeq	0.078	0.003	0.083
truncate_seq	0.002	0.000	0.003
trypsinCleave	0.104	0.003	0.108
uniqueJuncAnn	0.106	0.002	0.110
write.files	0.065	0.001	0.066
xCodons	0.025	0.003	0.028
xJunc	0.030	0.001	0.031
xJuncStrand	0.030	0.001	0.034