BioC 2.14: CHECK report for spliceSites on zin2

Package: spliceSites

Version: 1.2.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.2.0.tar.gz

StartedAt: 2014-10-08 03:00:43 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:03:40 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 176.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spliceSites.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.0’
* 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 ... [17s/18s] 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

* installing *source* package ‘spliceSites’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -std=gnu99 -shared -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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	0.000	0.000	0.002
aaGapSites-class	0.240	0.012	0.265
addGeneAlignPart	0.076	0.000	0.075
addHbond	0.476	0.008	0.507
addMaxEnt	0.516	0.000	0.547
alt_X_ranks	0.020	0.000	0.022
annGapSites-class	0.088	0.004	0.097
annotate-ExpressionSet	0.160	0.000	0.164
annotation	0.048	0.000	0.048
cRanges-class	0.052	0.000	0.053
caRanges-class	0.108	0.004	0.118
cdRanges-class	0.664	0.008	0.704
countByGeneName	0.084	0.004	0.087
dnaGapSites-class	0.504	0.004	0.524
dnaRanges	0.284	0.008	0.291
extractByGeneName	0.240	0.004	0.254
extractRange	0.032	0.000	0.032
gapSites-class	0.060	0.000	0.071
gapSites	0.140	0.008	0.160
getGapSites	0.052	0.004	0.061
hbond-class	0.012	0.000	0.011
keyProfiler-class	0.020	0.000	0.023
lrCodons	0.040	0.000	0.043
maxEnt-class	0.024	0.000	0.023
rangeByGeneName	0.040	0.000	0.039
readCuffGeneFpkm	0.080	0.000	0.081
readExpSet	0.108	0.000	0.107
readMergedBamGaps	0.032	0.000	0.030
readTabledBamGaps	0.068	0.000	0.066
silic_tryp	0.004	0.000	0.002
spliceSites-package	0.072	0.004	0.077
trim	0.036	0.004	0.041
truncateSeq	0.096	0.000	0.099
truncate_seq	0.000	0.000	0.002
trypsinCleave	0.104	0.000	0.106
uniqueJuncAnn	0.132	0.000	0.150
write.files	0.084	0.004	0.090
xCodons	0.036	0.000	0.038
xJunc	0.032	0.004	0.035
xJuncStrand	0.028	0.004	0.033