Mohamed Nadhir Djekidel
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/R3CPET |
| Branch: RELEASE_3_6 |
| Last Commit: 9d7fb65 |
| Last Changed Date: 2017-10-30 12:40:51 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:35 -0400 (Thu, 12 Apr 2018).
| Package 1109/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| R3CPET 1.10.0 Mohamed Nadhir Djekidel
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: R3CPET |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings R3CPET_1.10.0.tar.gz |
| StartedAt: 2018-04-12 02:06:59 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:11:35 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 276.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R3CPET.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings R3CPET_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/R3CPET.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 ‘R3CPET’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
data 3.0Mb
example 1.0Mb
libs 1.7Mb
* 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
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
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 use Fortran I/O
nor system RNGs.
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-3.6-bioc/meat/R3CPET.Rcheck/00check.log’
for details.
R3CPET.Rcheck/00install.out
* installing *source* package ‘R3CPET’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c corpus.cpp -o corpus.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c main.cpp -o main.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c stirln.cpp -o stirln.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/R3CPET.Rcheck/R3CPET/libs
** R
** data
** inst
** preparing 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)
R3CPET.Rcheck/tests/tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
0.164 0.024 0.188
R3CPET.Rcheck/R3CPET-Ex.timings
| name | user | system | elapsed | |
| Biogrid | 1.220 | 0.012 | 1.231 | |
| ChiapetExperimentData-class | 0.004 | 0.000 | 0.001 | |
| ChromMaintainers-class | 0.000 | 0.000 | 0.001 | |
| CreateCenteredBED-methods | 0.012 | 0.000 | 0.011 | |
| EnsemblToHGNC | 0 | 0 | 0 | |
| EntrezToHGNC | 0 | 0 | 0 | |
| GOEnrich-methods | 0.000 | 0.000 | 0.002 | |
| GenerateNetworks-methods | 0.000 | 0.000 | 0.002 | |
| HLDAResult-class | 0.000 | 0.000 | 0.001 | |
| HPRD | 0.212 | 0.004 | 0.217 | |
| InferNetworks-methods | 0.000 | 0.000 | 0.001 | |
| NetworkCollection-class | 0.000 | 0.000 | 0.001 | |
| PrepareData-methods | 0.000 | 0.000 | 0.001 | |
| RPKMS | 0.052 | 0.000 | 0.054 | |
| annotateExpression-methods | 0.004 | 0.000 | 0.002 | |
| buildNetworks-methods | 0.000 | 0.000 | 0.002 | |
| chromosoms | 0.004 | 0.000 | 0.002 | |
| cluesOrSota-class | 0.000 | 0.004 | 0.001 | |
| clusterInteractions-methods | 0.048 | 0.000 | 0.048 | |
| createIndexes-methods | 0.000 | 0.000 | 0.002 | |
| createServer-methods | 0.000 | 0.000 | 0.002 | |
| geneLocations | 0.132 | 0.000 | 0.130 | |
| getRegionsInNetwork-methods | 0.000 | 0.000 | 0.001 | |
| getRegionsIncluster-methods | 0.000 | 0.000 | 0.002 | |
| loadPETs-methods | 0.472 | 0.012 | 0.485 | |
| loadPPI-methods | 0.552 | 0.004 | 0.556 | |
| loadTFBS-methods | 0.516 | 0.000 | 0.519 | |
| outputGenesPerClusterToDir-methods | 0.000 | 0.000 | 0.002 | |
| outputGenesPerNetworkToDir-methods | 0.004 | 0.000 | 0.001 | |
| plotRes-methods | 0.000 | 0.000 | 0.002 | |
| plotTrack | 0.000 | 0.000 | 0.001 | |
| updateResults-methods | 0.004 | 0.000 | 0.002 | |
| visualizeCircos-methods | 0.000 | 0.000 | 0.001 | |
| visualizeInteractions-methods | 0.000 | 0.000 | 0.002 | |