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CHECK report for Harman on veracruz1

This page was generated on 2018-04-12 13:42:53 -0400 (Thu, 12 Apr 2018).

Package 638/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harman 1.6.0
Jason Ross
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Harman
Branch: RELEASE_3_6
Last Commit: 7b830b6
Last Changed Date: 2017-10-30 12:41:16 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Harman
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Harman_1.6.0.tar.gz
StartedAt: 2018-04-12 04:58:40 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 05:00:04 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 83.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Harman.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Harman_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Harman.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harman/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Harman’ version ‘1.6.0’
* 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 ‘Harman’ 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
* 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 ... 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

Harman.Rcheck/00install.out

* installing *source* package ‘Harman’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fPIC  -Wall -g -O2  -c Harman.cpp -o Harman.o
In file included from Harman.cpp:182:
./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable]
                 size_t currindex ;
                        ^
./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable]
                        double time1, time2 ;
                               ^
./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable]
                        double time1, time2 ;
                                      ^
./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                             ^
./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                        ^
./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable]
                                size_t randData1, randData2  ;
                                                  ^
6 warnings generated.
clang++ -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 -o Harman.so Harman.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/Harman.Rcheck/Harman/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Harman)

Tests output

Harman.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> BiocGenerics:::testPackage("Harman")


RUNIT TEST PROTOCOL -- Thu Apr 12 04:59:59 2018 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Harman RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 34.122   0.764  35.583 

Example timings

Harman.Rcheck/Harman-Ex.timings

nameusersystemelapsed
arrowPlot0.7750.0390.828
harman1.1620.0331.218
harmanresults0.7890.0280.825
pcaPlot0.6100.0370.665
plot.harmanresults0.5630.0250.594
prcompPlot0.3090.0320.351
reconstructData0.6940.0410.738
shiftBetas0.0030.0010.002
summary.harmanresults0.6770.0300.715