BioC 3.0: CHECK report for PING on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PING_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/PING.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [34s/35s] OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  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:
  ‘BSgenome’ ‘BiocGenerics’ ‘fda’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘IRanges’ ‘chipseq’
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/19s] 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
  ‘/home/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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ping.c -o ping.o
ping.c: In function ‘fitModelAllk’:
ping.c:145:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c: In function ‘iterEM’:
ping.c:659:25: warning: unused variable ‘mu’ [-Wunused-variable]
ping.c: In function ‘ECM1’:
ping.c:912:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:1072:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:760:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘ECM1PE’:
ping.c:1320:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:1473:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:1108:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘ECM2’:
ping.c:1536:66: warning: unused variable ‘ee’ [-Wunused-variable]
ping.c:1536:57: warning: unused variable ‘ggR’ [-Wunused-variable]
ping.c:1536:52: warning: unused variable ‘ggF’ [-Wunused-variable]
ping.c:1536:47: warning: unused variable ‘aaR’ [-Wunused-variable]
ping.c:1536:42: warning: unused variable ‘aaF’ [-Wunused-variable]
ping.c:1536:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
ping.c:1536:9: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
ping.c:1527:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘ECM2PE’:
ping.c:1743:66: warning: unused variable ‘ee’ [-Wunused-variable]
ping.c:1743:57: warning: unused variable ‘ggR’ [-Wunused-variable]
ping.c:1743:52: warning: unused variable ‘ggF’ [-Wunused-variable]
ping.c:1743:47: warning: unused variable ‘aaR’ [-Wunused-variable]
ping.c:1743:42: warning: unused variable ‘aaF’ [-Wunused-variable]
ping.c:1743:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
ping.c:1734:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘getInfMat’:
ping.c:2590:80: warning: unused variable ‘PhiRw’ [-Wunused-variable]
ping.c:2590:73: warning: unused variable ‘PhiFw’ [-Wunused-variable]
ping.c: In function ‘getInfMatPE’:
ping.c:3040:59: warning: unused variable ‘PhiFRw’ [-Wunused-variable]
ping.c: In function ‘mergePeak’:
ping.c:3312:20: warning: variable ‘tstatMax’ set but not used [-Wunused-but-set-variable]
ping.c:3301:11: warning: unused variable ‘j’ [-Wunused-variable]
ping.c:3301:7: warning: unused variable ‘i’ [-Wunused-variable]
ping.c: In function ‘BIC’:
ping.c:2101:6: warning: ‘penalty’ may be used uninitialized in this function [-Wuninitialized]
ping.c: In function ‘BICPE’:
ping.c:2208:6: warning: ‘penalty’ may be used uninitialized in this function [-Wuninitialized]
ping.c: In function ‘fitModelK’:
ping.c:477:18: warning: ‘firstFit’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o PING.so init.o ping.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/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	0.000	0.000	0.002
pingError-class	0.004	0.000	0.004
pingList-class	0.004	0.000	0.002
segmentPING	1.189	0.004	1.902

BioC 3.0: CHECK report for PING on zin1

Summary

Command output