Aaron Taudt
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/methimpute |
| Branch: master |
| Last Commit: fe2e049 |
| Last Changed Date: 2019-01-04 13:38:50 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:34:11 -0400 (Tue, 09 Apr 2019).
| Package 955/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methimpute 1.5.1 Aaron Taudt
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: methimpute |
| Version: 1.5.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methimpute.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methimpute_1.5.1.tar.gz |
| StartedAt: 2019-04-09 04:08:18 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:13:40 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 322.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: methimpute.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methimpute.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methimpute_1.5.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/methimpute.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methimpute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methimpute' version '1.5.1'
* 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 ... OK
* 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 ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/methimpute/libs/i386/methimpute.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/methimpute/libs/x64/methimpute.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'methimpute-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotting
> ### Title: Methimpute plotting functions
> ### Aliases: plotting plotHistogram plotScatter plotTransitionProbs
> ### plotConvergence plotEnrichment plotPosteriorDistance
>
> ### ** Examples
>
> ## Get some toy data
> file <- system.file("data","arabidopsis_toydata.RData",
+ package="methimpute")
> data <- get(load(file))
> print(data)
GRanges object with 200000 ranges and 2 metadata columns:
seqnames ranges strand | context counts
<Rle> <IRanges> <Rle> | <factor> <matrix>
[1] chr1 1 + | CHH 1:1
[2] chr1 2 + | CHH 1:1
[3] chr1 3 + | CHH 1:1
[4] chr1 8 + | CHH 1:1
[5] chr1 9 + | CHH 1:1
... ... ... ... . ... ...
[199996] chr1 533605 - | CHH 1:1
[199997] chr1 533608 - | CHH 1:1
[199998] chr1 533609 - | CHH 1:1
[199999] chr1 533611 - | CHH 1:2
[200000] chr1 533614 + | CG 0:23
-------
seqinfo: 7 sequences from an unspecified genome
> model <- callMethylation(data)
Adding distance ... 0.02s
Adding transition context ... 0.08s
Baum-Welch: Fitting HMM parameters
Iteration log(P) dlog(P) Time in sec
0 -inf - 0
1 -160163.727642 inf 0
2 -127777.227663 32386.499980 1
3 -126035.966931 1741.260732 2
4 -125702.635067 333.331863 3
5 -125628.276291 74.358776 3
6 -125606.740310 21.535981 4
7 -125600.011941 6.728368 5
8 -125597.765188 2.246753 6
9 -125596.967885 0.797304 7
HMM: Convergence reached!
Time spent in Baum-Welch: 7.18s
Compiling results ... 1.02s
> ## Make nice plots
> plotHistogram(model, total.counts=5)
> plotScatter(model)
> plotTransitionProbs(model)
> plotConvergence(model)
> plotPosteriorDistance(model$data)
Plotting maximum posterior vs. distance to nearest covered ... 1.99s
>
> ## Get annotation data and make an enrichment profile
> # Note that this looks a bit ugly because our toy data
> # has only 200000 datapoints.
> data(arabidopsis_genes)
> plotEnrichment(model, annotation=arabidopsis_genes)
Upstream and downstream counts for context CG
category none
Upstream and downstream counts for context CHG
category none
Upstream and downstream counts for context CHH
category none
Inside counts for context CG
category none
Error: memory exhausted (limit reached?)
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotting 17.39 1.97 18.85
extractCytosinesFromFASTA 5.78 0.64 6.42
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/methimpute.Rcheck/00check.log'
for details.
methimpute.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methimpute_1.5.1.tar.gz && rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methimpute.buildbin-libdir methimpute_1.5.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methimpute_1.5.1.zip && rm methimpute_1.5.1.tar.gz methimpute_1.5.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1283k 100 1283k 0 0 17.8M 0 --:--:-- --:--:-- --:--:-- 20.2M
install for i386
* installing *source* package 'methimpute' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c densities.cpp -o densities.o
densities.cpp: In member function 'virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)':
densities.cpp:614:138: warning: 'prob_context' may be used uninitialized in this function [-Wmaybe-uninitialized]
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);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c fitHMM.cpp -o fitHMM.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c fitHMM_context.cpp -o fitHMM_context.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c hmm_context.cpp -o hmm_context.o
hmm_context.cpp: In destructor 'HMM_context::˜HMM_context()':
hmm_context.cpp:68:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<this->emissionDensities.size(); i++)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c methimpute_init.c -o methimpute_init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp: In destructor 'ScaleHMM::˜ScaleHMM()':
scalehmm.cpp:311:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<this->emissionDensities.size(); i++)
^
C:/Rtools/mingw_32/bin/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/methimpute.buildbin-libdir/00LOCK-methimpute/00new/methimpute/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'methimpute'
finding HTML links ... done
arabidopsis_TEs html
arabidopsis_chromosomes html
arabidopsis_genes html
arabidopsis_toydata html
binning html
binomialTestMethylation html
callMethylation html
callMethylationSeparate html
collapseBins html
distanceCorrelation html
estimateTransDist html
exportMethylome html
extractCytosinesFromFASTA html
finding level-2 HTML links ... done
getDistinctColors html
getPosteriors html
getStateColors html
import html
importRene html
inflateMethylome html
loadFromFiles html
methimpute-objects html
methimpute-package html
methimputeBinomialHMM html
methimputeData html
parameterScan html
plotting html
print.methimputeBinomialHMM html
transCoord html
** 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
install for x64
* installing *source* package 'methimpute' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c densities.cpp -o densities.o
densities.cpp: In member function 'virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)':
densities.cpp:614:138: warning: 'prob_context' may be used uninitialized in this function [-Wmaybe-uninitialized]
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);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c fitHMM.cpp -o fitHMM.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c fitHMM_context.cpp -o fitHMM_context.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c hmm_context.cpp -o hmm_context.o
hmm_context.cpp: In destructor 'HMM_context::˜HMM_context()':
hmm_context.cpp:68:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<this->emissionDensities.size(); i++)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c methimpute_init.c -o methimpute_init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -mtune=generic -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp: In destructor 'ScaleHMM::˜ScaleHMM()':
scalehmm.cpp:311:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<this->emissionDensities.size(); i++)
^
C:/Rtools/mingw_64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/methimpute.buildbin-libdir/methimpute/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methimpute' as methimpute_1.5.1.zip
* DONE (methimpute)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'methimpute' successfully unpacked and MD5 sums checked
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methimpute.Rcheck/examples_i386/methimpute-Ex.timings
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methimpute.Rcheck/examples_x64/methimpute-Ex.timings
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