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 11:49:19 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings methimpute_1.5.1.tar.gz |
| StartedAt: 2019-04-09 01:52:13 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:54:55 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 162.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methimpute.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings methimpute_1.5.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/methimpute.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methimpute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methimpute’ version ‘1.5.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methimpute’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
libs 4.1Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotting 16.995 1.664 18.274
extractCytosinesFromFASTA 7.376 0.752 8.137
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-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-3.9-bioc/R/bin/R CMD INSTALL methimpute
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘methimpute’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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 BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)’:
densities.cpp:614:31: 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);
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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:68:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<this->emissionDensities.size(); i++)
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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:311:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i<this->emissionDensities.size(); i++)
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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 | 0.07 | 0.00 | 0.07 | |
| arabidopsis_chromosomes | 0.005 | 0.000 | 0.005 | |
| arabidopsis_genes | 0.02 | 0.00 | 0.02 | |
| arabidopsis_toydata | 0.261 | 0.015 | 0.277 | |
| binning | 3.393 | 0.037 | 3.430 | |
| binomialTestMethylation | 0.621 | 0.016 | 0.637 | |
| callMethylation | 3.499 | 0.003 | 3.049 | |
| callMethylationSeparate | 4.086 | 0.023 | 3.826 | |
| collapseBins | 3.909 | 0.004 | 3.914 | |
| distanceCorrelation | 1.614 | 0.028 | 1.654 | |
| estimateTransDist | 1.461 | 0.004 | 1.466 | |
| exportMethylome | 3.015 | 0.045 | 2.397 | |
| extractCytosinesFromFASTA | 7.376 | 0.752 | 8.137 | |
| getDistinctColors | 0.024 | 0.004 | 0.028 | |
| getStateColors | 0.018 | 0.000 | 0.017 | |
| import | 0.492 | 0.056 | 0.559 | |
| importRene | 0.048 | 0.004 | 0.053 | |
| inflateMethylome | 0.484 | 0.048 | 0.513 | |
| loadFromFiles | 0.164 | 0.000 | 0.165 | |
| plotting | 16.995 | 1.664 | 18.274 | |