Aaron Taudt
| Snapshot Date: 2024-05-26 14:00:09 -0400 (Sun, 26 May 2024) |
| git_url: https://git.bioconductor.org/packages/methimpute |
| git_branch: RELEASE_3_19 |
| git_last_commit: 515e616 |
| git_last_commit_date: 2024-04-30 11:01:18 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-27 11:35:25 -0400 (Mon, 27 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4752 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4517 |
| 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 1228/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methimpute 1.26.0 (landing page) Aaron Taudt
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.26.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings methimpute_1.26.0.tar.gz |
| StartedAt: 2024-05-27 00:20:31 -0400 (Mon, 27 May 2024) |
| EndedAt: 2024-05-27 00:24:03 -0400 (Mon, 27 May 2024) |
| EllapsedTime: 212.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methimpute.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings methimpute_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/methimpute.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘methimpute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methimpute’ 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 ‘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-3.19-bioc/meat/methimpute.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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 15.626 0.228 15.514
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/methimpute.Rcheck/00check.log’
for details.
methimpute.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL methimpute
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘methimpute’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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 in this function [-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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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 | 0.057 | 0.016 | 0.074 | |
| arabidopsis_chromosomes | 0.004 | 0.000 | 0.004 | |
| arabidopsis_genes | 0.014 | 0.004 | 0.017 | |
| arabidopsis_toydata | 0.148 | 0.008 | 0.155 | |
| binning | 2.577 | 0.096 | 2.674 | |
| binomialTestMethylation | 0.209 | 0.004 | 0.214 | |
| callMethylation | 3.004 | 0.080 | 2.786 | |
| callMethylationSeparate | 3.850 | 0.064 | 3.545 | |
| collapseBins | 2.007 | 0.048 | 2.055 | |
| distanceCorrelation | 1.455 | 0.040 | 1.494 | |
| estimateTransDist | 1.188 | 0.076 | 1.264 | |
| exportMethylome | 0 | 0 | 0 | |
| extractCytosinesFromFASTA | 4.769 | 0.060 | 4.830 | |
| getDistinctColors | 0.017 | 0.004 | 0.021 | |
| getStateColors | 0.013 | 0.000 | 0.013 | |
| import | 0.522 | 0.008 | 0.532 | |
| importRene | 0.039 | 0.000 | 0.040 | |
| inflateMethylome | 0.757 | 0.027 | 0.785 | |
| loadFromFiles | 0.137 | 0.012 | 0.149 | |
| plotting | 15.626 | 0.228 | 15.514 | |