Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1217/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methimpute 1.28.0 (landing page) Aaron Taudt
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the methimpute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methimpute.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: methimpute |
Version: 1.28.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings methimpute_1.28.0.tar.gz |
StartedAt: 2024-12-20 02:25:11 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:32:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 417.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: methimpute.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings methimpute_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘methimpute/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methimpute’ version ‘1.28.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘methimpute’ can be installed ... WARNING Found the following significant warnings: densities.cpp:920:105: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] See ‘/home/biocbuild/bbs-3.20-bioc/meat/methimpute.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 C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: libs 5.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: INITIAL RELEASE * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) methimputeBinomialHMM.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:28: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotting 14.942 0.087 14.664 * 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: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck/00check.log’ for details.
methimpute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL methimpute ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘methimpute’ ... ** 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’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c densities.cpp -o densities.o densities.cpp: In member function ‘virtual void NegativeBinomial::calc_densities(Rcpp::Matrix<14>::Row&)’: densities.cpp:920:105: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] 920 | if (verbosity>=4) Rprintf(" lGammaR = %g, lgamma(size + obs=%d) = %g\n", lGammaR, obs_j, lgamma(size + obs_j)); | ~^ ~~~~~ | | | | int double | %f densities.cpp: In member function ‘virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)’: densities.cpp:614:52: warning: ‘prob_context’ may be used uninitialized [-Wmaybe-uninitialized] 614 | if (verbosity >= 4) Rprintf("obs_test[t=%d] = %d, obs_total[t] = %d, prob_context = %g\n", t, obs_test[t], obs_total[t], prob_context); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ densities.cpp:599:16: note: ‘prob_context’ was declared here 599 | double prob_context; | ^~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c fitHMM.cpp -o fitHMM.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c fitHMM_context.cpp -o fitHMM_context.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c hmm_context.cpp -o hmm_context.o hmm_context.cpp: In destructor ‘HMM_context::~HMM_context()’: hmm_context.cpp:68:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Density*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for (int i=0; i<this->emissionDensities.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c methimpute_init.c -o methimpute_init.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c scalehmm.cpp -o scalehmm.o scalehmm.cpp: In destructor ‘ScaleHMM::~ScaleHMM()’: scalehmm.cpp:311:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Density*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 311 | for (int i=0; i<this->emissionDensities.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-methimpute/00new/methimpute/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (methimpute)
methimpute.Rcheck/methimpute-Ex.timings
name | user | system | elapsed | |
arabidopsis_TEs | 0.047 | 0.000 | 0.047 | |
arabidopsis_chromosomes | 0.003 | 0.000 | 0.003 | |
arabidopsis_genes | 0.014 | 0.001 | 0.016 | |
arabidopsis_toydata | 0.140 | 0.014 | 0.154 | |
binning | 2.933 | 0.110 | 3.043 | |
binomialTestMethylation | 0.199 | 0.006 | 0.204 | |
callMethylation | 2.999 | 0.014 | 2.598 | |
callMethylationSeparate | 3.590 | 0.027 | 3.201 | |
collapseBins | 2.261 | 0.035 | 2.296 | |
distanceCorrelation | 1.105 | 0.019 | 1.125 | |
estimateTransDist | 1.182 | 0.010 | 1.193 | |
exportMethylome | 0 | 0 | 0 | |
extractCytosinesFromFASTA | 4.813 | 0.054 | 4.867 | |
getDistinctColors | 0.019 | 0.000 | 0.019 | |
getStateColors | 0.013 | 0.000 | 0.013 | |
import | 0.472 | 0.001 | 0.474 | |
importRene | 0.038 | 0.001 | 0.040 | |
inflateMethylome | 0.784 | 0.037 | 0.821 | |
loadFromFiles | 0.145 | 0.004 | 0.149 | |
plotting | 14.942 | 0.087 | 14.664 | |