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This page was generated on 2015-10-20 16:12:53 -0400 (Tue, 20 Oct 2015).
| Package 198/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| CNPBayes 1.0.0 Jacob Carey
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK | ||||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: CNPBayes |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNPBayes_1.0.0.tar.gz |
| StartedAt: 2015-10-20 06:51:48 -0400 (Tue, 20 Oct 2015) |
| EndedAt: 2015-10-20 07:01:25 -0400 (Tue, 20 Oct 2015) |
| EllapsedTime: 577.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CNPBayes.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNPBayes_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CNPBayes.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNPBayes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNPBayes’ version ‘1.0.0’
* 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 ‘CNPBayes’ can be installed ... [104s/106s] 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
* 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 ... NOTE
coerce,MixtureModel-SummarizedExperiment: no visible global function
definition for ‘Rle’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
marginalLikelihood-method 12.411 0.122 12.541
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [234s/242s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
pos x y diff
1 0.299 0.320 -0.02047
2 0.168 0.206 -0.03822
3 0.148 0.145 0.00308
testthat results ================================================================
OK: 127 SKIPPED: 0 FAILED: 1
1. Failure (at test_marginal.R#33): test_marginal_hard
Error: testthat unit tests failed
In addition: Warning message:
In rnorm(k(object), mu(object), tau(object)) : NAs produced
Execution halted
* 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/CNPBayes.Rcheck/00check.log’
for details.
CNPBayes.Rcheck/tests/testthat.Rout.fail:
R version 3.2.2 Patched (2015-10-08 r69496) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CNPBayes)
Loading required package: foreach
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:testthat':
compare
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
> test_check("CNPBayes")
1. Failure (at test_marginal.R#33): test_marginal_hard -------------------------
sigma(truth) not equal to colMeans(sigmac(model))[i]
3/3 mismatches (average diff: 0.0206).
First 3:
pos x y diff
1 0.299 0.320 -0.02047
2 0.168 0.206 -0.03822
3 0.148 0.145 0.00308
testthat results ================================================================
OK: 127 SKIPPED: 0 FAILED: 1
1. Failure (at test_marginal.R#33): test_marginal_hard
Error: testthat unit tests failed
In addition: Warning message:
In rnorm(k(object), mu(object), tau(object)) : NAs produced
Execution halted
CNPBayes.Rcheck/00install.out:
* installing *source* package ‘CNPBayes’ ... ** libs llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c miscfunctions.cpp -o miscfunctions.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o reduced_pooledvariance.cpp: In function ‘Rcpp::NumericVector full_theta_pooled(Rcpp::S4)’: reduced_pooledvariance.cpp:46: warning: unused variable ‘prod’ reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_sigma_pooled(Rcpp::S4)’: reduced_pooledvariance.cpp:86: warning: unused variable ‘K’ reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_pi_pooled(Rcpp::S4)’: reduced_pooledvariance.cpp:242: warning: unused variable ‘K’ reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_mu_pooled(Rcpp::S4)’: reduced_pooledvariance.cpp:331: warning: unused variable ‘K’ reduced_pooledvariance.cpp: In function ‘Rcpp::NumericVector p_nu0_reduced_pooled(Rcpp::S4)’: reduced_pooledvariance.cpp:618: warning: unused variable ‘N’ reduced_pooledvariance.cpp: In function ‘Rcpp::S4 reduced_s20_pooled(Rcpp::S4)’: reduced_pooledvariance.cpp:683: warning: unused variable ‘K’ llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c update.cpp -o update.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c updates_batch.cpp -o updates_batch.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c updates_marginal.cpp -o updates_marginal.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c updates_reduced_batch.cpp -o updates_reduced_batch.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CNPBayes.so RcppExports.o miscfunctions.o reduced_pooledvariance.o singlebatch_pooledvar.o update.o updates_batch.o updates_marginal.o updates_reduced_batch.o updates_reduced_marginal.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.2-bioc/meat/CNPBayes.Rcheck/CNPBayes/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (CNPBayes)
CNPBayes.Rcheck/CNPBayes-Ex.timings:
| name | user | system | elapsed | |
| BatchModel | 0.049 | 0.001 | 0.050 | |
| DensityModel-class | 0.912 | 0.026 | 0.940 | |
| DensityModel | 0.008 | 0.000 | 0.009 | |
| Hyperparameters | 0.002 | 0.001 | 0.003 | |
| HyperparametersBatch | 0.002 | 0.000 | 0.003 | |
| HyperparametersMarginal | 0.006 | 0.001 | 0.006 | |
| MarginalModel | 0.018 | 0.000 | 0.018 | |
| McmcParams-class | 0.01 | 0.00 | 0.01 | |
| McmcParams | 0.003 | 0.001 | 0.003 | |
| batch-method | 0.019 | 0.007 | 0.027 | |
| bic-method | 0.005 | 0.000 | 0.005 | |
| burnin-method | 0.002 | 0.000 | 0.002 | |
| chains-method | 0.007 | 0.001 | 0.008 | |
| chromosome | 0.000 | 0.000 | 0.001 | |
| clusters-method | 0.447 | 0.003 | 0.451 | |
| collapseBatch-method | 0.046 | 0.001 | 0.046 | |
| consensusCNP | 1.820 | 0.064 | 1.885 | |
| eta.0-method | 0.001 | 0.000 | 0.001 | |
| hyperParams-method | 0.003 | 0.000 | 0.003 | |
| iter-method | 0.001 | 0.000 | 0.002 | |
| k-method | 0.018 | 0.000 | 0.018 | |
| logPrior-method | 0.001 | 0.001 | 0.002 | |
| log_lik-method | 0.002 | 0.000 | 0.003 | |
| m2.0-method | 0.001 | 0.001 | 0.002 | |
| map | 0.041 | 0.007 | 0.048 | |
| marginalLikelihood-method | 12.411 | 0.122 | 12.541 | |
| mcmcParams-method | 0.002 | 0.000 | 0.002 | |
| modes-method | 0.000 | 0.001 | 0.001 | |
| mu-method | 0.001 | 0.000 | 0.001 | |
| muMean | 0.002 | 0.001 | 0.001 | |
| muc | 0.001 | 0.000 | 0.001 | |
| nStarts-method | 0.003 | 0.000 | 0.002 | |
| nu.0-method | 0.001 | 0.000 | 0.000 | |
| p | 0.000 | 0.000 | 0.001 | |
| pic | 0.001 | 0.000 | 0.001 | |
| plot | 4.296 | 0.115 | 4.415 | |
| probz-method | 0.026 | 0.037 | 0.064 | |
| qInverseTau2 | 0.014 | 0.000 | 0.014 | |
| sigma | 0.001 | 0.001 | 0.001 | |
| sigma2-method | 0.002 | 0.000 | 0.001 | |
| sigma2.0-method | 0.001 | 0.001 | 0.001 | |
| sigmac | 0.001 | 0.000 | 0.001 | |
| simulateBatchData | 0.081 | 0.000 | 0.082 | |
| simulateData | 0.075 | 0.000 | 0.075 | |
| tau | 0.001 | 0.000 | 0.002 | |
| tau2-method | 0.011 | 0.001 | 0.013 | |
| tauMean | 0.001 | 0.000 | 0.002 | |
| tauc | 0.001 | 0.000 | 0.001 | |
| theta-method | 0.013 | 0.002 | 0.015 | |
| thin-method | 0.002 | 0.000 | 0.002 | |
| tracePlot-method | 0.116 | 0.008 | 0.133 | |
| y-method | 0.009 | 0.012 | 0.021 | |
| z-method | 0.004 | 0.008 | 0.013 | |
| zfreq-method | 0.002 | 0.000 | 0.002 | |