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This page was generated on 2024-03-27 11:36:57 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 1207/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methimpute 1.25.0  (landing page)
Aaron Taudt
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/methimpute
git_branch: devel
git_last_commit: 76fb513
git_last_commit_date: 2023-10-24 11:00:17 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for methimpute on nebbiolo1


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.

raw results


Summary

Package: methimpute
Version: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2024-03-27 00:01:16 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 00:04:53 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 216.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: methimpute.Rcheck
Warnings: 1

Command output

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### Running 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_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/methimpute.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘1.25.0’
* 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 16.051  0.216   15.87
* 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.


Installation output

methimpute.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL methimpute
###
##############################################################################
##############################################################################


* 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)

Tests output


Example timings

methimpute.Rcheck/methimpute-Ex.timings

nameusersystemelapsed
arabidopsis_TEs0.0510.0000.052
arabidopsis_chromosomes0.0020.0020.005
arabidopsis_genes0.0180.0000.018
arabidopsis_toydata0.1510.0040.155
binning2.8460.1242.971
binomialTestMethylation0.2040.0080.213
callMethylation2.7720.0832.482
callMethylationSeparate3.7860.0683.558
collapseBins2.3330.0442.377
distanceCorrelation1.2060.0241.230
estimateTransDist1.2450.0361.281
exportMethylome000
extractCytosinesFromFASTA4.8150.0364.852
getDistinctColors0.0210.0000.020
getStateColors0.0130.0000.013
import0.7860.0330.821
importRene0.0380.0040.042
inflateMethylome0.4400.0240.464
loadFromFiles0.1410.0080.150
plotting16.051 0.21615.870