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BioC 3.2: CHECK report for CNVtools on zin1

This page was generated on 2016-04-23 10:11:18 -0700 (Sat, 23 Apr 2016).

Package 203/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVtools 1.64.0
Chris Barnes
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CNVtools
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNVtools
Version: 1.64.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CNVtools_1.64.0.tar.gz
StartedAt: 2016-04-22 23:22:39 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:24:14 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 94.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNVtools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CNVtools_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CNVtools.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.64.0’
* 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 ... [7s/8s] 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 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 compiled code ... WARNING
File ‘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, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/55s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNVtest.select.model 30.473  0.024  30.510
CNVtest.binary        6.378  0.004   6.384
cnv.plot              6.224  0.016   6.246
qt.plot               5.068  0.000   5.070
CNVtest.qt            5.054  0.007   5.064
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/CNVtools.Rcheck/00check.log’
for details.


CNVtools.Rcheck/00install.out:

* installing *source* package ‘CNVtools’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fitmodel.cpp -o fitmodel.o
g++ -I/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mla.cpp -o mla.o
g++ -I/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c zeroin.c -o zeroin.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o CNVtools.so fitmodel.o glm_test.o mla.o routine.o zeroin.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/CNVtools.Rcheck/CNVtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNVtools)

CNVtools.Rcheck/CNVtools-Ex.timings:

nameusersystemelapsed
CNVtest.binary6.3780.0046.384
CNVtest.qt5.0540.0075.064
CNVtest.select.model30.473 0.02430.510
cnv.plot6.2240.0166.246
qt.plot5.0680.0005.070