BioC 3.2: CHECK report for spliceSites on oaxaca

Package: spliceSites

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.8.0.tar.gz

StartedAt: 2015-10-27 08:11:48 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:14:30 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 161.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spliceSites.Rcheck

Warnings: 1

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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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/spliceSites.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.8.0’
* 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 ... [16s/17s] 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 ... [11s/11s] 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-3.2-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-3.2-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing 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	0.000
aaGapSites-class	0.438	0.004	0.467
addGeneAlignPart	0.061	0.002	0.063
addHbond	0.252	0.018	0.270
addMaxEnt	0.262	0.004	0.266
alt_X_ranks	0.019	0.001	0.019
annGapSites-class	0.073	0.002	0.075
annotate-ExpressionSet	0.155	0.003	0.158
annotation	0.033	0.000	0.034
cRanges-class	0.043	0.002	0.045
caRanges-class	0.091	0.003	0.093
cdRanges-class	0.809	0.074	0.883
countByGeneName	0.066	0.002	0.067
dnaGapSites-class	0.231	0.006	0.238
dnaRanges	0.246	0.010	0.260
extractByGeneName	0.198	0.003	0.201
extractRange	0.028	0.003	0.031
gapSites-class	0.049	0.002	0.052
gapSites	0.120	0.002	0.121
getGapSites	0.050	0.001	0.052
hbond-class	0.007	0.001	0.007
keyProfiler-class	0.021	0.000	0.021
lrCodons	0.036	0.001	0.037
maxEnt-class	0.022	0.002	0.023
rangeByGeneName	0.029	0.001	0.030
readCuffGeneFpkm	0.082	0.001	0.083
readExpSet	0.087	0.002	0.087
readMergedBamGaps	0.019	0.001	0.020
readTabledBamGaps	0.064	0.001	0.066
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.057	0.001	0.059
trim	0.034	0.002	0.036
truncateSeq	0.078	0.004	0.082
truncate_seq	0.001	0.000	0.001
trypsinCleave	0.088	0.001	0.089
uniqueJuncAnn	0.132	0.002	0.134
write.files	0.056	0.002	0.057
xCodons	0.022	0.002	0.024
xJunc	0.031	0.001	0.033
xJuncStrand	0.031	0.001	0.032