BioC 3.0: CHECK report for spliceSites on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spliceSites_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/spliceSites.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘rbamtools’ ‘refGenome’ ‘doBy’ ‘Biobase’ ‘Biostrings’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [22s/24s] 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 ... WARNING
Codoc mismatches from documentation object 'readCuffGeneFpkm':
readCuffGeneFpkm
  Code: function(cuff, phenoData, summ = "max")
  Docs: function(cuff, phenoData)
  Argument names in code not in docs:
    summ

* 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 ... [15s/15s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

* installing *source* package ‘spliceSites’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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-3.0-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
* DONE (spliceSites)

name	user	system	elapsed
SpliceCountSet-class	0.000	0.000	0.001
aaGapSites-class	0.496	0.006	0.542
addGeneAlignPart	0.082	0.006	0.088
addHbond	0.482	0.007	0.492
addMaxEnt	0.324	0.010	0.334
alt_X_ranks	0.021	0.001	0.022
annGapSites-class	0.301	0.005	0.307
annotate-ExpressionSet	0.168	0.003	0.170
annotation	0.048	0.006	0.053
cRanges-class	0.058	0.005	0.063
caRanges-class	0.101	0.003	0.105
cdRanges-class	0.634	0.087	0.723
countByGeneName	0.089	0.003	0.092
dnaGapSites-class	0.277	0.013	0.290
dnaRanges	0.280	0.011	0.295
extractByGeneName	0.226	0.005	0.231
extractRange	0.032	0.002	0.034
gapSites-class	0.057	0.003	0.060
gapSites	0.370	0.005	0.377
getGapSites	0.058	0.003	0.062
hbond-class	0.010	0.001	0.011
keyProfiler-class	0.024	0.001	0.025
lrCodons	0.044	0.001	0.046
maxEnt-class	0.020	0.002	0.022
rangeByGeneName	0.039	0.002	0.041
readCuffGeneFpkm	0.085	0.006	0.092
readExpSet	0.123	0.005	0.129
readMergedBamGaps	0.029	0.002	0.031
readTabledBamGaps	0.071	0.003	0.075
silic_tryp	0.003	0.000	0.003
spliceSites-package	0.072	0.005	0.077
trim	0.042	0.003	0.045
truncateSeq	0.096	0.005	0.101
truncate_seq	0.002	0.000	0.003
trypsinCleave	0.113	0.002	0.116
uniqueJuncAnn	0.129	0.003	0.133
write.files	0.082	0.002	0.084
xCodons	0.031	0.002	0.034
xJunc	0.035	0.001	0.037
xJuncStrand	0.037	0.003	0.041

BioC 3.0: CHECK report for spliceSites on oaxaca

Summary

Command output