Aaron Taudt
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/methimpute |
| Branch: RELEASE_3_10 |
| Last Commit: 67c8034 |
| Last Changed Date: 2019-10-29 13:10:49 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:19 -0400 (Wed, 15 Apr 2020).
| Package 1013/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methimpute 1.8.0 Aaron Taudt
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: methimpute |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings methimpute_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:10:47 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:13:59 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 191.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methimpute.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:methimpute.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings methimpute_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/methimpute.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
libs 4.4Mb
* 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 23.844 0.024 24.396
extractCytosinesFromFASTA 9.088 0.012 9.366
callMethylationSeparate 5.428 0.032 5.752
* 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-3.10-bioc/meat/methimpute.Rcheck/00check.log’
for details.
methimpute.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL methimpute
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘methimpute’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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 | 0.08 | 0.00 | 0.08 | |
| arabidopsis_chromosomes | 0.004 | 0.000 | 0.004 | |
| arabidopsis_genes | 0.024 | 0.000 | 0.023 | |
| arabidopsis_toydata | 0.256 | 0.016 | 0.278 | |
| binning | 3.992 | 0.072 | 4.238 | |
| binomialTestMethylation | 0.352 | 0.008 | 0.405 | |
| callMethylation | 3.704 | 0.024 | 3.891 | |
| callMethylationSeparate | 5.428 | 0.032 | 5.752 | |
| collapseBins | 4.428 | 0.008 | 4.517 | |
| distanceCorrelation | 1.912 | 0.016 | 1.949 | |
| estimateTransDist | 2.084 | 0.020 | 2.219 | |
| exportMethylome | 0 | 0 | 0 | |
| extractCytosinesFromFASTA | 9.088 | 0.012 | 9.366 | |
| getDistinctColors | 0.036 | 0.000 | 0.039 | |
| getStateColors | 0.024 | 0.000 | 0.023 | |
| import | 0.840 | 0.008 | 0.909 | |
| importRene | 0.068 | 0.000 | 0.109 | |
| inflateMethylome | 0.620 | 0.016 | 0.666 | |
| loadFromFiles | 0.276 | 0.004 | 0.280 | |
| plotting | 23.844 | 0.024 | 24.396 | |