BioC 3.2: CHECK report for R3CPET on oaxaca

Package: R3CPET

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R3CPET_1.2.0.tar.gz

StartedAt: 2016-04-23 03:27:01 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:32:50 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 348.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: R3CPET.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R3CPET_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/R3CPET.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R3CPET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R3CPET’ version ‘1.2.0’
* 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 ‘R3CPET’ can be installed ... [52s/61s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
* 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
.GetClusterInfo: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
.GetClusterInfo: no visible global function definition for ‘toTable’
.GetClusterInfo: no visible binding for global variable
  ‘org.Hs.egUCSCKG’
.GetClusterInfo: no visible global function definition for ‘select’
.GetClusterInfo: no visible binding for global variable ‘org.Hs.eg.db’
.formatDAVIDResult: no visible global function definition for
  ‘formatGeneReportFull’
.formatDAVIDResult: no visible global function definition for
  ‘formatGeneReport’
.formatDAVIDResult: no visible global function definition for
  ‘formatList’
.formatDAVIDResult: no visible global function definition for
  ‘formatGene2Gene’
.formatDAVIDResult: no visible global function definition for
  ‘formatAnnotationReport’
.get.NetworksGenes: no visible global function definition for
  ‘annotatePeakInBatch’
EnsemblToHGNC: no visible global function definition for ‘useMart’
EnsemblToHGNC: no visible global function definition for ‘useDataset’
EnsemblToHGNC: no visible global function definition for ‘getBM’
EntrezToHGNC: no visible global function definition for ‘useMart’
EntrezToHGNC: no visible global function definition for ‘useDataset’
EntrezToHGNC: no visible global function definition for ‘getBM’
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
  no visible global function definition for ‘runApp’
plotTrack,ChiapetExperimentData-GRanges: no visible global function
  definition for ‘keepSeqlevels’
plotTrack,ChiapetExperimentData-GRanges: no visible global function
  definition for ‘seqlevels’
plotTrack,ChiapetExperimentData-GRanges: no visible global function
  definition for ‘seqlengths<-’
plotTrack,ChiapetExperimentData-GRanges: no visible global function
  definition for ‘seqlengths’
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
  .local: no visible global function definition for ‘keepSeqlevels’
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
  .local: no visible global function definition for ‘seqlevels’
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
  .local: no visible global function definition for ‘seqlengths<-’
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
  .local: no visible global function definition for ‘seqlengths’
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
  function definition for ‘keepSeqlevels’
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
  function definition for ‘seqlevels’
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
  function definition for ‘seqlengths<-’
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
  function definition for ‘seqlengths’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotRes-methods.Rd':
  ‘ggplot2’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 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 ... [19s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [0s/0s]
 [1s/1s] 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/R3CPET.Rcheck/00check.log’
for details.

* installing *source* package ‘R3CPET’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R3CPET_init.c -o R3CPET_init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c corpus.cpp -o corpus.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c main.cpp -o main.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c state.cpp -o state.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c stirln.cpp -o stirln.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.cpp -o utils.o
utils.cpp:5:14: warning: unused variable 'half_ln_2pi' [-Wunused-const-variable]
const double half_ln_2pi = 0.91893853320467267;
             ^
1 warning generated.
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 R3CPET.so R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/R3CPET.Rcheck/R3CPET/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
* DONE (R3CPET)

name	user	system	elapsed
Biogrid	1.172	0.023	1.196
ChiapetExperimentData-class	0.002	0.001	0.002
ChromMaintainers-class	0.002	0.000	0.002
CreateCenteredBED-methods	0.017	0.001	0.017
EnsemblToHGNC	0.001	0.000	0.001
EntrezToHGNC	0.001	0.001	0.001
GOEnrich-methods	0.003	0.000	0.003
GenerateNetworks-methods	0.002	0.001	0.002
HLDAResult-class	0.001	0.000	0.001
HPRD	0.100	0.011	0.110
InferNetworks-methods	0.003	0.000	0.003
NetworkCollection-class	0.001	0.001	0.002
PrepareData-methods	0.002	0.000	0.003
RPKMS	0.063	0.006	0.069
annotateExpression-methods	0.003	0.001	0.003
buildNetworks-methods	0.002	0.000	0.003
chromosoms	0.004	0.004	0.008
cluesOrSota-class	0.001	0.001	0.002
clusterInteractions-methods	0.058	0.004	0.063
createIndexes-methods	0.003	0.001	0.003
createServer-methods	0.002	0.000	0.033
geneLocations	0.103	0.007	0.110
getRegionsInNetwork-methods	0.003	0.000	0.003
getRegionsIncluster-methods	0.002	0.001	0.003
loadPETs-methods	0.319	0.008	0.327
loadPPI-methods	0.593	0.035	0.628
loadTFBS-methods	1.246	0.021	1.268
outputGenesPerClusterToDir-methods	0.002	0.001	0.002
outputGenesPerNetworkToDir-methods	0.003	0.000	0.004
plotRes-methods	0.003	0.001	0.004
plotTrack	0.002	0.000	0.003
updateResults-methods	0.001	0.000	0.002
visualizeCircos-methods	0.003	0.000	0.003
visualizeInteractions-methods	0.002	0.000	0.003