BioC 3.1: CHECK report for spliceSites on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/spliceSites.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ... [23s/24s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
dnaGapSites,gapSites : .local: no visible global function definition
  for ‘RleViewsList’
dnaRanges,cRanges : .local: no visible binding for global variable
  ‘TRUE...’
* 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 ... [16s/17s] 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

* installing *source* package ‘spliceSites’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c spliceSites.c -o spliceSites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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-3.1-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (spliceSites)

name	user	system	elapsed
SpliceCountSet-class	0.000	0.000	0.001
aaGapSites-class	0.704	0.006	0.740
addGeneAlignPart	0.100	0.003	0.102
addHbond	0.351	0.033	0.383
addMaxEnt	0.446	0.007	0.454
alt_X_ranks	0.024	0.001	0.025
annGapSites-class	0.111	0.012	0.123
annotate-ExpressionSet	0.166	0.002	0.169
annotation	0.058	0.001	0.060
cRanges-class	0.073	0.004	0.077
caRanges-class	0.131	0.004	0.135
cdRanges-class	0.965	0.141	1.108
countByGeneName	0.114	0.002	0.117
dnaGapSites-class	0.392	0.007	0.401
dnaRanges	0.806	0.017	0.828
extractByGeneName	0.312	0.003	0.314
extractRange	0.037	0.002	0.039
gapSites-class	0.080	0.003	0.084
gapSites	0.208	0.006	0.215
getGapSites	0.082	0.003	0.085
hbond-class	0.017	0.000	0.017
keyProfiler-class	0.033	0.000	0.033
lrCodons	0.058	0.002	0.059
maxEnt-class	0.034	0.003	0.037
rangeByGeneName	0.046	0.001	0.047
readCuffGeneFpkm	0.114	0.002	0.117
readExpSet	0.138	0.003	0.141
readMergedBamGaps	0.039	0.002	0.041
readTabledBamGaps	0.088	0.004	0.092
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.098	0.008	0.105
trim	0.050	0.002	0.053
truncateSeq	0.129	0.004	0.133
truncate_seq	0.004	0.000	0.004
trypsinCleave	0.120	0.005	0.125
uniqueJuncAnn	0.169	0.003	0.172
write.files	0.108	0.002	0.110
xCodons	0.034	0.001	0.035
xJunc	0.040	0.002	0.042
xJuncStrand	0.041	0.001	0.043

BioC 3.1: CHECK report for spliceSites on petty

Summary

Command output