BioC 3.2: CHECK report for spliceSites on oaxaca

Package: spliceSites

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.7.0.tar.gz

StartedAt: 2015-08-24 04:08:17 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:11:14 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 177.3 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_1.7.0.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 ‘1.7.0’
* 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/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 ... [12s/12s] 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	0	0
aaGapSites-class	0.434	0.003	0.498
addGeneAlignPart	0.064	0.001	0.066
addHbond	0.257	0.018	0.275
addMaxEnt	0.291	0.005	0.297
alt_X_ranks	0.018	0.000	0.019
annGapSites-class	0.078	0.002	0.081
annotate-ExpressionSet	0.159	0.003	0.163
annotation	0.034	0.001	0.035
cRanges-class	0.047	0.003	0.050
caRanges-class	0.098	0.003	0.102
cdRanges-class	0.827	0.078	0.924
countByGeneName	0.078	0.002	0.081
dnaGapSites-class	0.276	0.005	0.285
dnaRanges	0.258	0.012	0.274
extractByGeneName	0.206	0.004	0.211
extractRange	0.027	0.002	0.029
gapSites-class	0.053	0.002	0.055
gapSites	0.133	0.003	0.136
getGapSites	0.051	0.001	0.052
hbond-class	0.008	0.001	0.009
keyProfiler-class	0.021	0.000	0.022
lrCodons	0.039	0.001	0.039
maxEnt-class	0.018	0.002	0.019
rangeByGeneName	0.030	0.001	0.031
readCuffGeneFpkm	0.080	0.001	0.082
readExpSet	0.106	0.005	0.113
readMergedBamGaps	0.024	0.000	0.025
readTabledBamGaps	0.060	0.001	0.061
silic_tryp	0.002	0.001	0.002
spliceSites-package	0.065	0.003	0.068
trim	0.036	0.002	0.037
truncateSeq	0.087	0.003	0.089
truncate_seq	0.003	0.000	0.003
trypsinCleave	0.092	0.002	0.095
uniqueJuncAnn	0.135	0.001	0.137
write.files	0.086	0.001	0.087
xCodons	0.028	0.001	0.028
xJunc	0.034	0.001	0.035
xJuncStrand	0.035	0.001	0.037