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BioC 3.4: CHECK report for Harman on malbec1

This page was generated on 2017-04-15 16:13:48 -0400 (Sat, 15 Apr 2017).

Package 580/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harman 1.2.0
Jason Ross
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Harman
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Harman
Version: 1.2.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Harman_1.2.0.tar.gz
StartedAt: 2017-04-14 23:08:12 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:09:16 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 64.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Harman.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Harman_1.2.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Harman.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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

Harman.Rcheck/00install.out:

* installing *source* package ‘Harman’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"  `/home/biocbuild/bbs-3.4-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fpic  -g -O2  -Wall -c Harman.cpp -o Harman.o
In file included from Harman.cpp:182:0:
CSelectRandom.h: In instantiation of ‘std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(std::size_t, std::size_t, std::size_t, std::size_t) [with T = double; std::size_t = long unsigned int]’:
Harman.cpp:1764:117:   required from here
CSelectRandom.h:943:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     while (currval < howManyIN)
                    ^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o Harman.so Harman.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

Harman.Rcheck/Harman-Ex.timings:

nameusersystemelapsed
arrowPlot0.7000.0040.848
harman0.8800.0120.893
harmanresults0.6840.0000.683
pcaPlot0.540.000.54
plot.harmanresults0.4840.0000.484
prcompPlot0.1840.0000.184
reconstructData0.6280.0080.637
shiftBetas0.0040.0000.001
summary.harmanresults0.5480.0000.550