Aaron Taudt
| Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024) |
| git_url: https://git.bioconductor.org/packages/methimpute |
| git_branch: devel |
| git_last_commit: 2e2fc1f |
| git_last_commit_date: 2024-04-30 11:01:18 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-22 11:37:00 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
| 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 1189/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methimpute 1.27.0 (landing page) Aaron Taudt
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.27.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methimpute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methimpute_1.27.0.tar.gz |
| StartedAt: 2024-05-21 02:22:12 -0400 (Tue, 21 May 2024) |
| EndedAt: 2024-05-21 02:25:19 -0400 (Tue, 21 May 2024) |
| EllapsedTime: 186.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methimpute.Rcheck |
| Warnings: 1 |
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### Running command:
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### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methimpute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methimpute_1.27.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'methimpute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methimpute' version '1.27.0'
* 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 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 'F:/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/methimpute/libs/x64/methimpute.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotting 20.16 0.40 20.13
extractCytosinesFromFASTA 5.80 0.22 6.04
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck/00check.log'
for details.
methimpute.Rcheck/00install.out
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### Running command:
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### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL methimpute
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'methimpute' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitHMM.cpp -o fitHMM.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitHMM_context.cpp -o fitHMM_context.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare]
68 | for (int i=0; i<this->emissionDensities.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c methimpute_init.c -o methimpute_init.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare]
311 | for (int i=0; i<this->emissionDensities.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o methimpute.dll tmp.def RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-methimpute/00new/methimpute/libs/x64
** 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
** 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 | 0.05 | 0.02 | 0.06 | |
| arabidopsis_chromosomes | 0.00 | 0.02 | 0.02 | |
| arabidopsis_genes | 0.01 | 0.00 | 0.01 | |
| arabidopsis_toydata | 0.14 | 0.00 | 0.14 | |
| binning | 3.21 | 0.17 | 3.38 | |
| binomialTestMethylation | 0.28 | 0.03 | 0.31 | |
| callMethylation | 3.51 | 0.11 | 3.15 | |
| callMethylationSeparate | 4.58 | 0.14 | 4.43 | |
| collapseBins | 3.20 | 0.11 | 3.32 | |
| distanceCorrelation | 1.15 | 0.14 | 1.28 | |
| estimateTransDist | 1.34 | 0.05 | 1.39 | |
| exportMethylome | 0 | 0 | 0 | |
| extractCytosinesFromFASTA | 5.80 | 0.22 | 6.04 | |
| getDistinctColors | 0.07 | 0.00 | 0.08 | |
| getStateColors | 0.02 | 0.00 | 0.02 | |
| import | 1.22 | 0.59 | 2.67 | |
| importRene | 0.06 | 0.04 | 0.09 | |
| inflateMethylome | 0.66 | 0.59 | 1.97 | |
| loadFromFiles | 0.17 | 0.05 | 0.22 | |
| plotting | 20.16 | 0.40 | 20.13 | |