R3CPET 1.4.2
Mohamed Nadhir Djekidel
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/R3CPET | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings R3CPET_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/R3CPET.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 ‘R3CPET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R3CPET’ version ‘1.4.2’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
data 3.0Mb
example 1.0Mb
libs 1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’
A package should be listed in only one of these fields.
* 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' 'GenomeInfoDb'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.DAVIDQuery: no visible global function definition for 'read.delim'
.DavidGOAnalysis: no visible global function definition for 'plot'
.DavidGOAnalysis.folder: no visible global function definition for
'read.csv'
.DavidGOAnalysis.folder: no visible global function definition for
'write.table'
.GetClusterInfo: no visible binding for global variable
'TxDb.Hsapiens.UCSC.hg19.knownGene'
.GetClusterInfo: no visible global function definition for
'subsetByOverlaps'
.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'
.ReadPET: no visible global function definition for 'read.table'
.ReadPET: no visible global function definition for 'head'
.ReadTFBS: no visible global function definition for 'read.table'
.ReadTFBS: no visible global function definition for 'head'
.RemoveOutliers: no visible global function definition for 'quantile'
.calculate.all.shortest.paths : <anonymous>: no visible global function
definition for 'tail'
.check.pet: no visible global function definition for 'mcols'
.check.tfbs: no visible global function definition for 'mcols'
.checkChIAPETFormat: no visible global function definition for
'read.table'
.create.datatables_chip: no visible global function definition for
'subjectHits'
.create.datatables_chip: no visible global function definition for
'queryHits'
.filterPPI: no visible global function definition for 'data'
.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.ClusterInvolvedGenes: no visible global function definition for
'write.table'
.get.NetworksGenes: no visible global function definition for
'annotatePeakInBatch'
.get.NetworksGenes: no visible global function definition for
'write.table'
.getNuclearPPI: no visible global function definition for 'data'
.plot.clustOrderHeatmap: no visible global function definition for
'colors'
.plot.clustOrderHeatmap: no visible global function definition for
'png'
.plot.clustOrderHeatmap: no visible global function definition for
'colorRampPalette'
.plot.clustOrderHeatmap: no visible global function definition for
'dev.off'
.plotAllNet: no visible global function definition for 'pdf'
.plotAllNet: no visible global function definition for 'plot'
.plotAllNet: no visible global function definition for 'dev.off'
.plotNetwork: no visible global function definition for 'gray'
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'
pet<-,ChiapetExperimentData: no visible global function definition for
'mcols'
plot3CPETRes,ChromMaintainers: no visible global function definition
for 'par'
plot3CPETRes,ChromMaintainers: no visible global function definition
for 'plot'
plotTrack,ChiapetExperimentData-GRanges: no visible global function
definition for 'subsetByOverlaps'
plotTrack,ChiapetExperimentData-GRanges: no visible global function
definition for 'data'
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'
tfbs<-,ChiapetExperimentData: no visible global function definition for
'mcols'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric: no
visible global function definition for 'keepSeqlevels'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric: no
visible global function definition for 'seqlevels'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric: no
visible global function definition for 'seqlengths<-'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric: no
visible global function definition for 'seqlengths'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric: no
visible global function definition for 'values'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric: no
visible global function definition for 'plot'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'subsetByOverlaps'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'data'
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'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'values'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'plot'
Undefined global functions or variables:
TxDb.Hsapiens.UCSC.hg19.knownGene annotatePeakInBatch
colorRampPalette colors data dev.off formatAnnotationReport
formatGene2Gene formatGeneReport formatGeneReportFull formatList
getBM gray head keepSeqlevels mcols org.Hs.eg.db org.Hs.egUCSCKG par
pdf plot png quantile queryHits read.csv read.delim read.table runApp
select seqlengths seqlengths<- seqlevels subjectHits subsetByOverlaps
tail toTable useDataset useMart values write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "colors", "dev.off",
"gray", "pdf", "png")
importFrom("graphics", "par", "plot")
importFrom("stats", "quantile")
importFrom("utils", "data", "head", "read.csv", "read.delim",
"read.table", "tail", "write.table")
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 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 ... NOTE
File ‘R3CPET/libs/R3CPET.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘state.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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 ‘tests.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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/R3CPET.Rcheck/00check.log’
for details.
* installing *source* package ‘R3CPET’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c R3CPET_init.c -o R3CPET_init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c corpus.cpp -o corpus.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c main.cpp -o main.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c state.cpp -o state.o
state.cpp: In member function ‘int HDP::sample_word_assignment(DocState*, int, bool, vct*)’:
state.cpp:251:45: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
doc_state->words_[i].topic_assignment_ = k;
^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c stirln.cpp -o stirln.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o R3CPET.so R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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 "IRanges" for requests: queryHits
No methods found in "IRanges" for requests: subjectHits
No methods found in "IRanges" for requests: elementLengths
No methods found in "GenomicRanges" for requests: mcols
No methods found in "GenomicRanges" for requests: values
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<-
No methods found in "GenomicRanges" for requests: subsetByOverlaps
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 "IRanges" for requests: queryHits
No methods found in "IRanges" for requests: subjectHits
No methods found in "IRanges" for requests: elementLengths
No methods found in "GenomicRanges" for requests: mcols
No methods found in "GenomicRanges" for requests: values
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<-
No methods found in "GenomicRanges" for requests: subsetByOverlaps
* DONE (R3CPET)