Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 |
Package 1636/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
R3CPET 1.39.0 (landing page) Mohamed Nadhir Djekidel
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the R3CPET package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R3CPET.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: R3CPET |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings R3CPET_1.39.0.tar.gz |
StartedAt: 2024-12-24 01:15:30 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 01:21:44 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 373.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: R3CPET.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings R3CPET_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/R3CPET.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘R3CPET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘R3CPET’ version ‘1.39.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘R3CPET’ can be installed ... WARNING Found the following significant warnings: state.cpp:171:29: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<DocState**, vector<DocState*> >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] state.cpp:173:27: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<WordInfo*, vector<WordInfo> >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] See ‘/home/biocbuild/bbs-3.21-bioc/meat/R3CPET.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 7.1Mb sub-directories of 1Mb or more: data 3.0Mb libs 1.4Mb * 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 code 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' .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 ... WARNING checkRd: (5) ChiapetExperimentData-class.Rd:109-124: \item in \describe must have non-empty label checkRd: (5) ChiapetExperimentData-class.Rd:125-128: \item in \describe must have non-empty label checkRd: (5) ChiapetExperimentData-class.Rd:129-132: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Biogrid.Rd: igraph ChiapetExperimentData-class.Rd: GRanges, GRanges-class, igraph ChromMaintainers-class.Rd: igraph GenerateNetworks-methods.Rd: igraph HPRD.Rd: igraph cluesOrSota-class.Rd: sota clusterInteractions-methods.Rd: sota createIndexes-methods.Rd: data.table-class getRegionsInNetwork-methods.Rd: GRanges getRegionsIncluster-methods.Rd: GRanges loadPETs-methods.Rd: GRanges-class loadPPI-methods.Rd: igraph loadTFBS-methods.Rd: GRanges-class plotRes-methods.Rd: sota, igraph, pheatmap, cluster visualizeCircos-methods.Rd: GRanges, ggplot visualizeInteractions-methods.Rd: GRanges, ggplot, ggbio Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 File ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 nor [v]sprintf. 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/R3CPET.Rcheck/00check.log’ for details.
R3CPET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL R3CPET ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘R3CPET’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c R3CPET_init.c -o R3CPET_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c corpus.cpp -o corpus.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c main.cpp -o main.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c state.cpp -o state.o state.cpp: In member function ‘int HDP::iterate_gibbs_state(bool, bool)’: state.cpp:171:29: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<DocState**, vector<DocState*> >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 171 | std::random_shuffle ( doc_states_.begin(), doc_states_.end() ); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from state.cpp:2: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ state.cpp:173:27: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<WordInfo*, vector<WordInfo> >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 173 | std::random_shuffle ( doc_states_[j]->words_.begin(), doc_states_[j]->words_.end() ); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ state.cpp: In member function ‘int HDP::sample_word_assignment(DocState*, int, bool, vct*)’: state.cpp:253:10: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 253 | return int(old_k != k); | ^~~~~~~~~~~~~~~ state.cpp:193:19: note: ‘k’ was declared here 193 | int old_k = -1, k; | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c stirln.cpp -o stirln.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c utils.cpp -o utils.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 0.137 0.038 0.165
R3CPET.Rcheck/R3CPET-Ex.timings
name | user | system | elapsed | |
Biogrid | 0.260 | 0.018 | 0.278 | |
ChiapetExperimentData-class | 0.001 | 0.001 | 0.001 | |
ChromMaintainers-class | 0.001 | 0.000 | 0.001 | |
CreateCenteredBED-methods | 0.009 | 0.001 | 0.009 | |
EnsemblToHGNC | 0.001 | 0.000 | 0.000 | |
EntrezToHGNC | 0.000 | 0.000 | 0.001 | |
GOEnrich-methods | 0.002 | 0.000 | 0.002 | |
GenerateNetworks-methods | 0.002 | 0.000 | 0.002 | |
HLDAResult-class | 0 | 0 | 0 | |
HPRD | 0.095 | 0.000 | 0.095 | |
InferNetworks-methods | 0.002 | 0.000 | 0.002 | |
NetworkCollection-class | 0 | 0 | 0 | |
PrepareData-methods | 0.002 | 0.000 | 0.001 | |
RPKMS | 0.051 | 0.001 | 0.053 | |
annotateExpression-methods | 0.002 | 0.000 | 0.002 | |
buildNetworks-methods | 0.001 | 0.000 | 0.001 | |
chromosoms | 0.001 | 0.002 | 0.002 | |
cluesOrSota-class | 0.000 | 0.001 | 0.000 | |
clusterInteractions-methods | 0.050 | 0.000 | 0.049 | |
createIndexes-methods | 0.001 | 0.001 | 0.001 | |
createServer-methods | 0.000 | 0.001 | 0.002 | |
geneLocations | 0.111 | 0.003 | 0.115 | |
getRegionsInNetwork-methods | 0.001 | 0.001 | 0.002 | |
getRegionsIncluster-methods | 0.002 | 0.000 | 0.001 | |
loadPETs-methods | 0.184 | 0.001 | 0.186 | |
loadPPI-methods | 0.574 | 0.015 | 0.590 | |
loadTFBS-methods | 1.403 | 0.006 | 1.411 | |
outputGenesPerClusterToDir-methods | 0.001 | 0.001 | 0.001 | |
outputGenesPerNetworkToDir-methods | 0.002 | 0.000 | 0.002 | |
plotRes-methods | 0.001 | 0.000 | 0.002 | |
plotTrack | 0.001 | 0.000 | 0.001 | |
updateResults-methods | 0.000 | 0.000 | 0.001 | |
visualizeCircos-methods | 0.001 | 0.001 | 0.001 | |
visualizeInteractions-methods | 0.002 | 0.000 | 0.001 | |