Elana J. Fertig
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CoGAPS |
| Branch: RELEASE_3_7 |
| Last Commit: 9d82c1f |
| Last Changed Date: 2018-07-26 15:59:34 -0400 (Thu, 26 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:23:10 -0400 (Wed, 17 Oct 2018).
| Package 287/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoGAPS 3.0.2 Elana J. Fertig
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CoGAPS |
| Version: 3.0.2 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CoGAPS_3.0.2.tar.gz |
| StartedAt: 2018-10-15 23:24:58 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:26:30 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 92.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CoGAPS_3.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CoGAPS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.0.2’
* 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 ‘CoGAPS’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
libs 9.7Mb
* 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 ... NOTE
GWCoGapsFromCheckpoint: no visible binding for global variable ‘i’
GWCoGapsFromCheckpoint: no visible binding for global variable
‘sampleS’
cellMatchR: no visible binding for global variable ‘cluster.method’
patternMatcher : <anonymous>: no visible binding for global variable
‘Samples’
patternMatcher : <anonymous>: no visible binding for global variable
‘value’
patternMatcher : <anonymous>: no visible binding for global variable
‘BySet’
runFinalPhase: no visible binding for global variable ‘i’
runFinalPhase: no visible binding for global variable ‘sampleS’
runInitialPhase: no visible binding for global variable ‘i’
runInitialPhase: no visible binding for global variable ‘sampleS’
scCoGapsFromCheckpoint: no visible binding for global variable ‘i’
scCoGapsFromCheckpoint: no visible binding for global variable
‘sampleS’
sc_runFinalPhase: no visible binding for global variable ‘i’
sc_runFinalPhase: no visible binding for global variable ‘sampleS’
sc_runInitialPhase: no visible binding for global variable ‘i’
sc_runInitialPhase: no visible binding for global variable ‘sampleS’
Undefined global functions or variables:
BySet Samples cluster.method i sampleS value
* 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
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/CoGAPS/libs/CoGAPS.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘srand’, possibly from ‘srand’ (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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotDiag 54.836 2.64 57.529
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.
CoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘CoGAPS’ ... ** libs g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Algorithms.cpp -o Algorithms.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c AtomicSupport.cpp -o AtomicSupport.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Cogaps.cpp -o Cogaps.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c GibbsSampler.cpp -o GibbsSampler.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Matrix.cpp -o Matrix.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Random.cpp -o Random.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.o g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o CoGAPS.so Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/CoGAPS/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 * DONE (CoGAPS)
CoGAPS.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(CoGAPS)
Loading required package: Rcpp
Attaching package: 'CoGAPS'
The following object is masked from 'package:stats':
residuals
>
> test_check("CoGAPS")
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
is a Catch v1.10.0 host application.
Run with -? for options
-------------------------------------------------------------------------------
Test GibbsSampler.h
GibbsSampler Statistics
-------------------------------------------------------------------------------
cpp_tests/testGibbsSampler.cpp:57
...............................................................................
cpp_tests/testGibbsSampler.cpp:105: FAILED:
REQUIRE( sampler.meanChiSq() == Approx(8371.568).epsilon(0.001) )
with expansion:
11813.07031f == Approx( 8371.568 )
===============================================================================
test cases: 7 | 6 passed | 1 failed
assertions: 94506 | 94505 passed | 1 failed
══ testthat results ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 2 FAILED: 0
>
> proc.time()
user system elapsed
1.396 0.080 1.484
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 0.492 | 0.000 | 0.489 | |
| GWCoGAPS | 0.200 | 0.028 | 0.141 | |
| GWCoGapsFromCheckpoint | 0.424 | 0.028 | 0.266 | |
| binaryA | 0.020 | 0.012 | 0.033 | |
| calcCoGAPSStat | 0.020 | 0.004 | 0.028 | |
| calcGeneGSStat | 0.016 | 0.004 | 0.022 | |
| calcZ | 0.004 | 0.000 | 0.002 | |
| computeGeneGSProb | 0.044 | 0.012 | 0.055 | |
| createGWCoGAPSSets | 0.008 | 0.000 | 0.005 | |
| createscCoGAPSSets | 0.004 | 0.000 | 0.006 | |
| displayBuildReport | 0.000 | 0.000 | 0.001 | |
| gapsMapRun | 0.452 | 0.000 | 0.450 | |
| gapsRun | 0.356 | 0.000 | 0.357 | |
| plotAtoms | 0.004 | 0.000 | 0.005 | |
| plotDiag | 54.836 | 2.640 | 57.529 | |
| plotGAPS | 0.012 | 0.004 | 0.015 | |
| plotP | 0.004 | 0.000 | 0.004 | |
| reconstructGene | 0.004 | 0.000 | 0.003 | |
| residuals | 0.032 | 0.000 | 0.031 | |