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BioC 2.13: CHECK report for bgx on zin1

This page was generated on 2014-04-05 09:47:28 -0700 (Sat, 05 Apr 2014).

Package 71/750HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.28.0
Ernest Turro
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/bgx
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: bgx
Version: 1.28.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings bgx_1.28.0.tar.gz
StartedAt: 2014-04-04 23:47:00 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:49:24 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 144.1 seconds
RetCode: 0
Status:  OK 
CheckDir: bgx.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/bgx.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bgx/DESCRIPTION’ ... OK
* this is package ‘bgx’ version ‘1.28.0’
* 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 ‘bgx’ can be installed ... [17s/17s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... NOTE
prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples
prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details
prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value
prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples
prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details
prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘bgx.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
bgx 50.619   0.16  51.349
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/bgx.Rcheck/00check.log’
for details.

bgx.Rcheck/00install.out:

* installing *source* package ‘bgx’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 206d7:2200800:1fbee3ff:bfebfbff
checking whether C compiler accepts -march=pentium-m... no
checking whether C compiler accepts -mcpu=pentium-m... no
checking whether C compiler accepts -mpentium-m... no
checking whether C compiler accepts -march=pentium3... no
checking whether C compiler accepts -mcpu=pentium3... no
checking whether C compiler accepts -mpentium3... no
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... no
checking whether C compiler accepts -mpentiumpro... no
checking for gcc architecture flag... unknown
checking for gcc -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -g -O2  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++ -shared -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
rm -r ../boostIncl
installing to /home/biocbuild/bbs-2.13-bioc/meat/bgx.Rcheck/bgx/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 (bgx)

bgx.Rcheck/bgx-Ex.timings:

nameusersystemelapsed
bgx50.619 0.16051.349