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Package 141/658HostnameOS / ArchBUILDCHECKBUILD BIN
CNVtools 1.53.0
Chris Barnes
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNVtools
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: CNVtools
Version: 1.53.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CNVtools_1.53.0.tar.gz
StartedAt: 2013-03-25 00:57:30 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:59:37 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 126.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNVtools.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CNVtools.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVtools’ version ‘1.53.0’
* 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 ‘CNVtools’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/home/biocbuild/bbs-2.12-bioc/meat/CNVtools.Rcheck/CNVtools/libs/CNVtools.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘fitmodel.o’, ‘routine.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘fitmodel.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘fitmodel.o’, ‘routine.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [90s/92s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNVtest.select.model 50.391  0.044  51.360
CNVtest.binary       11.200  0.032  11.826
cnv.plot             10.065  0.016  10.380
qt.plot               8.756  0.012   8.917
CNVtest.qt            8.569  0.004   8.592
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/CNVtools.Rcheck/00check.log’
for details.

CNVtools.Rcheck/00install.out:

* installing *source* package ‘CNVtools’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fitmodel.cpp -o fitmodel.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_test.cpp -o glm_test.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mla.cpp -o mla.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c routine.cpp -o routine.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c zeroin.c -o zeroin.o
g++ -shared -L/usr/local/lib -o CNVtools.so fitmodel.o glm_test.o mla.o routine.o zeroin.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/CNVtools.Rcheck/CNVtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘CNVtools-vignette.Rnw’ 
** testing if installed package can be loaded
* DONE (CNVtools)

CNVtools.Rcheck/CNVtools-Ex.timings:

nameusersystemelapsed
CNVtest.binary11.200 0.03211.826
CNVtest.qt8.5690.0048.592
CNVtest.select.model50.391 0.04451.360
cnv.plot10.065 0.01610.380
qt.plot8.7560.0128.917