BioC 3.3: CHECK report for spliceSites on morelia

Package: spliceSites

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spliceSites_1.19.0.tar.gz

StartedAt: 2016-04-21 07:50:54 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:53:09 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 134.4 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_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/spliceSites.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.19.0’
* 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 ... [13s/14s] 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 ... [9s/10s] 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	0.195	0.004	0.252
addGeneAligns	0.045	0.002	0.049
addHbond	0.412	0.006	0.419
addMaxEnt	0.281	0.020	0.302
alt_X_ranks	0.016	0.000	0.017
annGapSites-class	0.041	0.002	0.042
annotate-ExpressionSet	0.139	0.002	0.142
annotation	0.02	0.00	0.02
cRanges-class	0.046	0.003	0.050
caRanges-class	0.091	0.004	0.095
cdRanges-class	0.578	0.080	0.658
countByGeneName	0.076	0.002	0.078
dnaGapSites-class	0.204	0.004	0.209
dnaRanges	0.243	0.014	0.262
extractByGeneName	0.148	0.001	0.149
extractRange	0.016	0.001	0.017
gapSites-class	0.032	0.002	0.033
gapSites	0.101	0.003	0.104
getGapSites	0.049	0.001	0.050
hbond-class	0.009	0.001	0.008
keyProfiler-class	0.017	0.000	0.018
lrCodons	0.035	0.001	0.036
maxEnt-class	0.016	0.001	0.016
plotGeneAlignDepth	0.078	0.003	0.082
rangeByGeneName	0.028	0.001	0.028
readCuffGeneFpkm	0.066	0.001	0.067
readExpSet	0.082	0.002	0.083
readMergedBamGaps	0.023	0.001	0.024
readTabledBamGaps	0.038	0.001	0.039
seqlogo	0.110	0.005	0.116
silic_tryp	0.002	0.000	0.002
spliceSites-package	0.042	0.002	0.044
trim	0.029	0.002	0.031
truncateSeq	0.069	0.003	0.071
truncate_seq	0.002	0.000	0.003
trypsinCleave	0.087	0.001	0.088
uniqueJuncAnn	0.100	0.001	0.101
write.files	0.064	0.001	0.064
xCodons	0.033	0.001	0.033
xJunc	0.028	0.001	0.028
xJuncStrand	0.030	0.001	0.032