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CHECK report for R3CPET on malbec1

This page was generated on 2019-04-16 11:51:17 -0400 (Tue, 16 Apr 2019).

Package 1238/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R3CPET 1.14.0
Mohamed Nadhir Djekidel
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/R3CPET
Branch: RELEASE_3_8
Last Commit: 78d0702
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: R3CPET
Version: 1.14.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings R3CPET_1.14.0.tar.gz
StartedAt: 2019-04-16 02:21:26 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:26:55 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 328.8 seconds
RetCode: 0
Status:  OK 
CheckDir: R3CPET.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings R3CPET_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/R3CPET.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
    libs      1.8Mb
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  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
.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'
Undefined global functions or variables:
  TxDb.Hsapiens.UCSC.hg19.knownGene annotatePeakInBatch
  formatAnnotationReport formatGene2Gene formatGeneReport
  formatGeneReportFull formatList getBM org.Hs.eg.db org.Hs.egUCSCKG
  runApp select toTable useDataset useMart
* 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
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/R3CPET/libs/R3CPET.so’:
  Found ‘rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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-3.8-bioc/meat/R3CPET.Rcheck/00check.log’
for details.



Installation output

R3CPET.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL R3CPET
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘R3CPET’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R3CPET_init.c -o R3CPET_init.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c corpus.cpp -o corpus.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c main.cpp -o main.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/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:253:20: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
                    ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c stirln.cpp -o stirln.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/R3CPET/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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
* DONE (R3CPET)

Tests output

R3CPET.Rcheck/tests/tests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> test_create_ChiapetExperimentData <- function(){
+     x <- ChiapetExperimentData()
+     checkTrue(class(x) == "ChiapetExperimentData", 
+                 "No problem creating ChiapetExperimentData ")
+ }
> 
> test_interactions_file <- function(){
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     
+     chechTrue(file.exists(petFile))
+ }
> 
> test_TFBS_file <- function(){
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     chechTrue(file.exists(tfFile))
+ }
> 
> test_loadPETS <- function(){
+     x <- ChiapetExperimentData()
+     checkEquals(class(x),"ChiapetExperimentData")
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     
+     test_interactions_file()
+     
+     x <- loadPETs(x,petFile=petFile, IsBed=FALSE)
+     
+     checkTrue(length(pet(x)) >0, "PETs can be loadded")
+ }
> 
> test_loadPETS <- function(){
+     x <- ChiapetExperimentData()
+     checkEquals(class(x),"ChiapetExperimentData")
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     
+     test_TFBS_file()
+     
+     x <- loadTFBS(x,tfbsFile= tfFile)
+     
+     checkTrue(length(tfbs(x)) >0, "TFBS can be loadded")
+ }
> 
> 
> test_createIndex <- function(){
+     x <- ChiapetExperimentData()
+     
+     
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     x <- loadTFBS(x,tfbsFile= tfFile)
+     
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     x <- loadPETs(x,petFile=petFile, IsBed=FALSE)
+     
+     x<- createIndexes(x)
+     
+     checkEquals(length(x@.dt),3)
+     checkIdentical(names(x@.dt), c("PET","motifs", "hasMotif"))
+     
+     for(i in 1:3) checkTrue("data.table" %in% class(x@.dt[[i]]) )
+ }
> 
> proc.time()
   user  system elapsed 
  0.208   0.028   0.255 

Example timings

R3CPET.Rcheck/R3CPET-Ex.timings

nameusersystemelapsed
Biogrid1.2680.0201.329
ChiapetExperimentData-class000
ChromMaintainers-class0.0000.0000.001
CreateCenteredBED-methods0.0160.0000.017
EnsemblToHGNC000
EntrezToHGNC000
GOEnrich-methods0.0000.0000.002
GenerateNetworks-methods0.0040.0000.001
HLDAResult-class000
HPRD0.0960.0000.160
InferNetworks-methods0.0000.0000.002
NetworkCollection-class0.0000.0000.001
PrepareData-methods0.0000.0000.002
RPKMS0.0680.0080.102
annotateExpression-methods0.0040.0000.002
buildNetworks-methods0.0000.0000.001
chromosoms0.0040.0000.003
cluesOrSota-class000
clusterInteractions-methods0.0680.0040.072
createIndexes-methods0.0000.0000.002
createServer-methods0.0040.0000.001
geneLocations0.1560.0040.232
getRegionsInNetwork-methods0.0000.0000.001
getRegionsIncluster-methods0.0040.0000.002
loadPETs-methods0.2440.0120.297
loadPPI-methods0.6400.0280.674
loadTFBS-methods0.5080.0080.529
outputGenesPerClusterToDir-methods0.0000.0040.002
outputGenesPerNetworkToDir-methods0.0000.0000.002
plotRes-methods0.0040.0000.002
plotTrack0.0000.0000.001
updateResults-methods0.0000.0000.002
visualizeCircos-methods0.0040.0000.001
visualizeInteractions-methods0.0000.0000.001