| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:36 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the R3CPET package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/R3CPET.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1515/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| R3CPET 1.26.0 (landing page) Mohamed Nadhir Djekidel
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: R3CPET |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R3CPET_1.26.0.tar.gz |
| StartedAt: 2022-04-12 17:16:14 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:23:56 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 461.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R3CPET.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R3CPET_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.0’
* 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 6.1Mb
sub-directories of 1Mb or more:
data 3.0Mb
example 1.0Mb
* 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'
.plot.sota: no visible global function definition for 'legend'
.plot.sota: no visible global function definition for 'lines'
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'
RunHLDA: no visible binding for global variable '_R3CPET_RunHLDA'
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
no visible global function definition for 'runApp'
plot3CPETRes,ChromMaintainers: no visible global function definition
for 'plotCurves'
plot3CPETRes,ChromMaintainers: no visible global function definition
for 'plotAvgCurves'
Undefined global functions or variables:
TxDb.Hsapiens.UCSC.hg19.knownGene _R3CPET_RunHLDA annotatePeakInBatch
formatAnnotationReport formatGene2Gene formatGeneReport
formatGeneReportFull formatList getBM legend lines org.Hs.eg.db
org.Hs.egUCSCKG plotAvgCurves plotCurves runApp select toTable
useDataset useMart
Consider adding
importFrom("graphics", "legend", "lines")
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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
‘/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.Rcheck/00check.log’
for details.
R3CPET.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL R3CPET
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘R3CPET’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R3CPET_init.c -o R3CPET_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c corpus.cpp -o corpus.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c main.cpp -o main.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c state.cpp -o state.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stirln.cpp -o stirln.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-R3CPET/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R3CPET)
R3CPET.Rcheck/tests/tests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.315 0.078 0.365
R3CPET.Rcheck/R3CPET-Ex.timings
| name | user | system | elapsed | |
| Biogrid | 1.223 | 0.015 | 1.238 | |
| ChiapetExperimentData-class | 0.001 | 0.001 | 0.001 | |
| ChromMaintainers-class | 0.001 | 0.001 | 0.002 | |
| CreateCenteredBED-methods | 0.013 | 0.002 | 0.015 | |
| EnsemblToHGNC | 0.000 | 0.001 | 0.001 | |
| EntrezToHGNC | 0 | 0 | 0 | |
| GOEnrich-methods | 0.002 | 0.001 | 0.003 | |
| GenerateNetworks-methods | 0.002 | 0.001 | 0.003 | |
| HLDAResult-class | 0.001 | 0.000 | 0.000 | |
| HPRD | 0.104 | 0.004 | 0.108 | |
| InferNetworks-methods | 0.002 | 0.001 | 0.002 | |
| NetworkCollection-class | 0.000 | 0.001 | 0.001 | |
| PrepareData-methods | 0.002 | 0.001 | 0.003 | |
| RPKMS | 0.074 | 0.004 | 0.077 | |
| annotateExpression-methods | 0.002 | 0.002 | 0.003 | |
| buildNetworks-methods | 0.002 | 0.001 | 0.003 | |
| chromosoms | 0.003 | 0.002 | 0.006 | |
| cluesOrSota-class | 0.001 | 0.001 | 0.001 | |
| clusterInteractions-methods | 0.070 | 0.004 | 0.073 | |
| createIndexes-methods | 0.001 | 0.001 | 0.003 | |
| createServer-methods | 0.002 | 0.001 | 0.003 | |
| geneLocations | 0.161 | 0.006 | 0.167 | |
| getRegionsInNetwork-methods | 0.002 | 0.001 | 0.003 | |
| getRegionsIncluster-methods | 0.002 | 0.001 | 0.002 | |
| loadPETs-methods | 0.345 | 0.010 | 0.355 | |
| loadPPI-methods | 0.618 | 0.026 | 0.645 | |
| loadTFBS-methods | 0.563 | 0.013 | 0.577 | |
| outputGenesPerClusterToDir-methods | 0.001 | 0.000 | 0.002 | |
| outputGenesPerNetworkToDir-methods | 0.001 | 0.001 | 0.003 | |
| plotRes-methods | 0.002 | 0.001 | 0.003 | |
| plotTrack | 0.002 | 0.000 | 0.002 | |
| updateResults-methods | 0.002 | 0.001 | 0.003 | |
| visualizeCircos-methods | 0.002 | 0.001 | 0.003 | |
| visualizeInteractions-methods | 0.002 | 0.001 | 0.003 | |