BioC 3.3: CHECK report for DNAcopy on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DNAcopy_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DNAcopy.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 ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.46.0’
* 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 ‘DNAcopy’ 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 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
plot.DNAcopy: no visible global function definition for ‘dev.cur’
plot.DNAcopy: no visible global function definition for ‘dev.new’
plot.DNAcopy: no visible global function definition for
  ‘dev.interactive’
segment: no visible global function definition for ‘data’
segment: no visible binding for global variable ‘default.DNAcopy.bdry’
Undefined global functions or variables:
  data default.DNAcopy.bdry dev.cur dev.interactive dev.new
Consider adding
  importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new")
  importFrom("utils", "data")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 ‘tests’ ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/DNAcopy.Rcheck/00check.log’
for details.

* installing *source* package ‘DNAcopy’ ...
** libs
gfortran   -fpic  -g -O2  -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:283:0: warning: ‘tmaxj’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       iseg(2) = tmaxj
 ^
cbsWtstats.f:282:0: warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       iseg(1) = tmaxi
 ^
gfortran   -fpic  -g -O2  -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:258:0: warning: ‘sxmxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                      tmaxj = sxmxi + i2j
 ^
gfortran   -fpic  -g -O2  -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran   -fpic  -g -O2  -Wall -c changepoints.f -o changepoints.o
gfortran   -fpic  -g -O2  -Wall -c esegment.f -o esegment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c flchoose.c -o flchoose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fphyper.c -o fphyper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fpnorm.c -o fpnorm.o
gfortran   -fpic  -g -O2  -Wall -c getbdry.f -o getbdry.o
gfortran   -fpic  -g -O2  -Wall -c prune.f -o prune.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rshared.c -o rshared.o
gfortran   -fpic  -g -O2  -Wall -c segmentp.f -o segmentp.o
gfortran   -fpic  -g -O2  -Wall -c smoothCNA.f -o smoothCNA.o
gfortran   -fpic  -g -O2  -Wall -c tailprobs.f -o tailprobs.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/DNAcopy.Rcheck/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DNAcopy)

name	user	system	elapsed
CNA	0.017	0.004	0.021
exon.segment	0.141	0.000	0.142
plot.DNAcopy	0.822	0.004	0.838
plotSample	0.695	0.004	0.711
segment	1.314	0.000	1.330
segments.p	0.067	0.000	0.067
segments.summary	0.065	0.001	0.065
smooth.CNA	0.010	0.000	0.011
subset.CNA	0.006	0.000	0.005
zoomIntoRegion	0.609	0.000	0.609

BioC 3.3: CHECK report for DNAcopy on zin2

Summary

Command output