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: 2019-03-18 05:16:23 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 05:19:50 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 207.9 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) (2019-01-22 r76000)
* 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	0.000	0.000	0.001
aaGapSites-class	0.841	0.023	0.871
addGeneAligns	0.095	0.004	0.100
addGenomeData-ExpressionSet	0.914	0.145	1.065
addGenomeData-gapSites	0.732	0.021	0.754
addHbond	0.208	0.012	0.221
addMaxEnt	0.300	0.017	0.319
alt_X_ranks	0.023	0.001	0.025
annGapSites-class	0.119	0.004	0.124
annotate-ExpressionSet	0.173	0.004	0.179
annotation	0.023	0.001	0.025
cRanges-class	0.050	0.005	0.056
caRanges-class	0.115	0.003	0.119
cdRanges-class	0.974	0.215	1.191
countByGeneName	0.104	0.003	0.109
dnaGapSites-class	0.324	0.008	0.333
dnaRanges	0.358	0.026	0.385
extractByGeneName	0.301	0.007	0.308
extractRange	0.031	0.003	0.036
gapSites-class	0.055	0.005	0.060
gapSites	0.104	0.008	0.112
getGapSites	0.068	0.008	0.076
hbond-class	0.006	0.000	0.007
keyProfiler-class	0.024	0.001	0.025
lrCodons	0.069	0.002	0.071
maxEnt-class	0.018	0.004	0.021
plotGeneAlignDepth	0.096	0.008	0.104
rangeByGeneName	0.065	0.002	0.068
readCuffGeneFpkm	0.073	0.004	0.081
readExpSet	0.103	0.003	0.106
readMergedBamGaps	0.030	0.002	0.032
readTabledBamGaps	0.214	0.006	0.219
seqlogo	0.199	0.022	0.221
silic_tryp	0.003	0.000	0.003
spliceSites-package	0.053	0.007	0.059
trim	0.044	0.005	0.048
truncateSeq	0.087	0.005	0.092
truncate_seq	0.003	0.001	0.003
trypsinCleave	0.090	0.006	0.096
uniqueJuncAnn	0.151	0.003	0.156
write.files	0.075	0.001	0.077
xCodons	0.028	0.001	0.030
xJunc	0.042	0.003	0.045
xJuncStrand	0.026	0.002	0.029