BioC 3.0: CHECK report for PING on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PING_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PING.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PING/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PING’ version ‘2.10.0’
* 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 ‘PING’ can be installed ... [56s/59s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘BSgenome’ ‘fda’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘chipseq’ ‘GenomicRanges’ ‘IRanges’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘parallel:::detectCores’ ‘parallel:::makeCluster’
  ‘parallel:::parLapply’ ‘parallel:::stopCluster’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CoverageTrack: no visible global function definition for ‘resize’
CoverageTrack: no visible global function definition for ‘seqnames’
CoverageTrack: no visible global function definition for ‘coverage’
CoverageTrack: no visible global function definition for ‘width’
RawReadsTrack: no visible global function definition for ‘seqnames’
RawReadsTrack: no visible global function definition for ‘strand’
segmentPING: no visible global function definition for ‘seqlevels’
segmentPING: no visible global function definition for ‘IRanges’
* 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 ... [27s/27s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/PING.Rcheck/00check.log’
for details.

* installing *source* package ‘PING’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ping.c -o ping.o
ping.c: In function ‘fitModelAllk’:
ping.c:145: warning: suggest parentheses around comparison in operand of &
ping.c: In function ‘iterEM’:
ping.c:659: warning: unused variable ‘mu’
ping.c: In function ‘ECM1’:
ping.c:912: warning: suggest parentheses around comparison in operand of &
ping.c:1072: warning: suggest parentheses around comparison in operand of &
ping.c:760: warning: unused variable ‘k’
ping.c: In function ‘ECM1PE’:
ping.c:1320: warning: suggest parentheses around comparison in operand of &
ping.c:1473: warning: suggest parentheses around comparison in operand of &
ping.c:1108: warning: unused variable ‘k’
ping.c: In function ‘ECM2’:
ping.c:1536: warning: unused variable ‘ee’
ping.c:1536: warning: unused variable ‘ggR’
ping.c:1536: warning: unused variable ‘ggF’
ping.c:1536: warning: unused variable ‘aaR’
ping.c:1536: warning: unused variable ‘aaF’
ping.c:1536: warning: unused variable ‘etaDiff’
ping.c:1527: warning: unused variable ‘k’
ping.c: In function ‘ECM2PE’:
ping.c:1743: warning: unused variable ‘ee’
ping.c:1743: warning: unused variable ‘ggR’
ping.c:1743: warning: unused variable ‘ggF’
ping.c:1743: warning: unused variable ‘aaR’
ping.c:1743: warning: unused variable ‘aaF’
ping.c:1743: warning: unused variable ‘etaDiff’
ping.c:1734: warning: unused variable ‘k’
ping.c: In function ‘getInfMat’:
ping.c:2590: warning: unused variable ‘PhiRw’
ping.c:2590: warning: unused variable ‘PhiFw’
ping.c: In function ‘getInfMatPE’:
ping.c:3040: warning: unused variable ‘PhiFRw’
ping.c: In function ‘mergePeak’:
ping.c:3301: warning: unused variable ‘j’
ping.c:3301: warning: unused variable ‘i’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o PING.so init.o ping.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/PING.Rcheck/PING/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
* DONE (PING)

name	user	system	elapsed
ping-class	0.001	0.000	0.002
pingError-class	0.005	0.000	0.004
pingList-class	0.003	0.001	0.003
segmentPING	1.215	0.065	1.294

BioC 3.0: CHECK report for PING on perceval

Summary

Command output