Mohamed Nadhir Djekidel
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/R3CPET |
| Branch: RELEASE_3_9 |
| Last Commit: 373413d |
| Last Changed Date: 2019-05-02 11:53:54 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:33:09 -0400 (Wed, 16 Oct 2019).
| Package 1301/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| R3CPET 1.16.0 Mohamed Nadhir Djekidel
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: R3CPET |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R3CPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings R3CPET_1.16.0.tar.gz |
| StartedAt: 2019-10-16 06:18:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:25:47 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 426.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R3CPET.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R3CPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings R3CPET_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/R3CPET.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R3CPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R3CPET' version '1.16.0'
* 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 whether package 'R3CPET' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
data 3.0Mb
example 1.0Mb
libs 1.6Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/R3CPET/libs/i386/R3CPET.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/R3CPET/libs/x64/R3CPET.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'tests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/R3CPET.Rcheck/00check.log'
for details.
R3CPET.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/R3CPET_1.16.0.tar.gz && rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=R3CPET.buildbin-libdir R3CPET_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL R3CPET_1.16.0.zip && rm R3CPET_1.16.0.tar.gz R3CPET_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 5377k 100 5377k 0 0 37.6M 0 --:--:-- --:--:-- --:--:-- 39.4M
install for i386
* installing *source* package 'R3CPET' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R3CPET_init.c -o R3CPET_init.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c corpus.cpp -o corpus.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c main.cpp -o main.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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);
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c stirln.cpp -o stirln.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/R3CPET.buildbin-libdir/00LOCK-R3CPET/00new/R3CPET/libs/i386
** 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
converting help for package 'R3CPET'
finding HTML links ... done
Biogrid html
finding level-2 HTML links ... done
ChiapetExperimentData-class html
ChromMaintainers-class html
CreateCenteredBED-methods html
EnsemblToHGNC html
EntrezToHGNC html
GOEnrich-methods html
GenerateNetworks-methods html
HLDAResult-class html
HPRD html
InferNetworks-methods html
NetworkCollection-class html
PrepareData-methods html
R3CPET-package html
RPKMS html
annotateExpression-methods html
buildNetworks-methods html
chromosoms html
cluesOrSota-class html
clusterInteractions-methods html
createIndexes-methods html
createServer-methods html
geneLocations html
getRegionsInNetwork-methods html
getRegionsIncluster-methods html
loadPETs-methods html
loadPPI-methods html
loadTFBS-methods html
outputGenesPerClusterToDir-methods html
outputGenesPerNetworkToDir-methods html
plotRes-methods html
plotTrack html
updateResults-methods html
visualizeCircos-methods html
visualizeInteractions-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'R3CPET' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R3CPET_init.c -o R3CPET_init.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c corpus.cpp -o corpus.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c main.cpp -o main.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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);
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c stirln.cpp -o stirln.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R3CPET' as R3CPET_1.16.0.zip
* DONE (R3CPET)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'R3CPET' successfully unpacked and MD5 sums checked
|
R3CPET.Rcheck/tests_i386/tests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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([email protected]),3)
+ checkIdentical(names([email protected]), c("PET","motifs", "hasMotif"))
+
+ for(i in 1:3) checkTrue("data.table" %in% class([email protected][[i]]) )
+ }
>
> proc.time()
user system elapsed
0.26 0.03 0.28
|
R3CPET.Rcheck/tests_x64/tests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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([email protected]),3)
+ checkIdentical(names([email protected]), c("PET","motifs", "hasMotif"))
+
+ for(i in 1:3) checkTrue("data.table" %in% class([email protected][[i]]) )
+ }
>
> proc.time()
user system elapsed
0.18 0.06 0.23
|
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R3CPET.Rcheck/examples_i386/R3CPET-Ex.timings
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R3CPET.Rcheck/examples_x64/R3CPET-Ex.timings
|