BioC 3.3: CHECK report for spliceSites on oaxaca

Package: spliceSites

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.20.0.tar.gz

StartedAt: 2016-10-13 06:35:02 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:37:24 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 142.5 seconds

RetCode: 0

Status:  OK

CheckDir: spliceSites.Rcheck

Warnings: 0

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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_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/spliceSites.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... 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 ... NOTE
readCuffGeneFpkm: no visible global function definition for
  ‘read.table’
plot_diff,annGapSites: no visible global function definition for ‘par’
plot_diff,annGapSites: no visible global function definition for
  ‘barplot’
plot_diff_ranks,gapSites: no visible global function definition for
  ‘par’
plot_diff_ranks,gapSites: no visible global function definition for
  ‘barplot’
write.annDNA.tables,gapSites-DNAStringSet-character: no visible global
  function definition for ‘write.table’
write.files,aaGapSites: no visible global function definition for
  ‘write.table’
write.files,caRanges: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  barplot par read.table write.table
Consider adding
  importFrom("graphics", "barplot", "par")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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-3.3-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	0.230	0.005	0.251
addGeneAligns	0.044	0.001	0.045
addHbond	0.223	0.004	0.226
addMaxEnt	0.450	0.003	0.452
alt_X_ranks	0.017	0.000	0.017
annGapSites-class	0.048	0.002	0.050
annotate-ExpressionSet	0.137	0.003	0.139
annotation	0.028	0.003	0.030
cRanges-class	0.049	0.007	0.056
caRanges-class	0.098	0.012	0.109
cdRanges-class	0.811	0.087	0.899
countByGeneName	0.073	0.002	0.074
dnaGapSites-class	0.223	0.004	0.227
dnaRanges	0.247	0.011	0.262
extractByGeneName	0.225	0.005	0.229
extractRange	0.022	0.001	0.023
gapSites-class	0.049	0.003	0.052
gapSites	0.134	0.002	0.136
getGapSites	0.059	0.002	0.061
hbond-class	0.008	0.000	0.009
keyProfiler-class	0.020	0.001	0.021
lrCodons	0.038	0.001	0.038
maxEnt-class	0.016	0.001	0.018
plotGeneAlignDepth	0.092	0.003	0.096
rangeByGeneName	0.032	0.000	0.032
readCuffGeneFpkm	0.072	0.003	0.075
readExpSet	0.081	0.001	0.082
readMergedBamGaps	0.023	0.001	0.024
readTabledBamGaps	0.061	0.002	0.063
seqlogo	0.179	0.008	0.188
silic_tryp	0.002	0.000	0.003
spliceSites-package	0.039	0.003	0.042
trim	0.023	0.002	0.024
truncateSeq	0.082	0.001	0.083
truncate_seq	0.002	0.000	0.003
trypsinCleave	0.096	0.004	0.100
uniqueJuncAnn	0.129	0.002	0.130
write.files	0.091	0.001	0.092
xCodons	0.029	0.001	0.030
xJunc	0.033	0.001	0.034
xJuncStrand	0.033	0.001	0.034