BioC 3.4: CHECK report for sapFinder on zin1

Package: sapFinder

Version: 1.11.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sapFinder_1.11.0.tar.gz

StartedAt: 2016-09-20 12:16:26 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:17:48 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 81.8 seconds

RetCode: 0

Status:  OK

CheckDir: sapFinder.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sapFinder_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/sapFinder.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sapFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sapFinder’ version ‘1.11.0’
* 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 ‘sapFinder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      1.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
.spplot: no visible global function definition for ‘mtext’
.spplot: no visible global function definition for ‘axis’
.spplot: no visible global function definition for ‘points’
Sys.which2: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  axis mtext points setNames
Consider adding
  importFrom("graphics", "axis", "mtext", "points")
  importFrom("stats", "setNames")
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
Examples with CPU or elapsed time > 5s
                user system elapsed
easyRun       11.664  3.336  12.162
reportCreator 11.356  3.200  11.898
parserGear     8.512  3.088   8.362
runTandem      6.376  2.708   7.284
dbCreator      5.764  2.848   6.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/sapFinder.Rcheck/00check.log’
for details.

* installing *source* package ‘sapFinder’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c dataHandle.cpp -o dataHandle.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o sapFinder.so dataHandle.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/sapFinder.Rcheck/sapFinder/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 (sapFinder)

name	user	system	elapsed
dbCreator	5.764	2.848	6.846
easyRun	11.664	3.336	12.162
parserGear	8.512	3.088	8.362
reportCreator	11.356	3.200	11.898
runTandem	6.376	2.708	7.284