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BioC 3.0: CHECK report for BGmix on zin1

This page was generated on 2015-04-10 09:37:58 -0700 (Fri, 10 Apr 2015).

Package 79/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BGmix 1.26.0
Alex Lewin
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BGmix
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: BGmix
Version: 1.26.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.26.0.tar.gz
StartedAt: 2015-04-09 21:52:28 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:53:28 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 60.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BGmix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/BGmix.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BGmix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BGmix’ version ‘1.26.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BGmix’ can be installed ... [9s/9s] 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 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘BGmix/libs/BGmix.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘updates_BGmix.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
FDRforTailPP 8.005  0.364   8.415
BGmix        5.412  0.076   5.529
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/BGmix.Rcheck/00check.log’
for details.

BGmix.Rcheck/00install.out:

* installing *source* package ‘BGmix’ ...
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 gcc -std=gnu99 option to accept ISO C99... none needed
checking for cos 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-3.0-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
BGmix_main.cpp: In function ‘void BGmix(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double*, double*, double*, int*, int&, double*, int*, char**, char**, char**, char**, char**)’:
BGmix_main.cpp:165:31: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BGmix_main.cpp:178:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BGmix_main.cpp:179:47: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BGmix_main.cpp:546:48: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
BGmix_main.cpp:621:48: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -DUSING_R -c rundir.cpp -o rundir.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fpic  -g -O2  -Wall -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
updates_BGmix.cpp: In function ‘void update_z_beta1_joint2(int*, double**, int*, int&, int&, double*, double&, double&, double**, double**, double**, int*, double**, double**, int&, int&, int&, int*, int&, int&, int&, Random&)’:
updates_BGmix.cpp:192:29: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:200:28: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp: In function ‘void predict(double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double*, double**, double*, double**, double**, double**, double**, double*, double*, int*, double**, double**, int*, double*, double&, double&, double&, double&, double&, int&, int&, int&, int&, int&, int*, int&, Random&)’:
updates_BGmix.cpp:870:41: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:883:46: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:883:67: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:893:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp: In function ‘void predict_t(double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double**, double*, double*, double*, int*, double**, double**, int*, double*, double&, double&, double&, double&, double&, int&, int&, int&, int&, int&, int*, int&, Random&)’:
updates_BGmix.cpp:995:41: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1008:46: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1008:67: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1018:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:989:5: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
rm -r ../boostIncl 
installing to /home/biocbuild/bbs-3.0-bioc/meat/BGmix.Rcheck/BGmix/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 (BGmix)

BGmix.Rcheck/BGmix-Ex.timings:

nameusersystemelapsed
BGmix-package2.3800.0562.461
BGmix5.4120.0765.529
EstimatePi03.3600.1603.532
FDRforTailPP8.0050.3648.415
FDRplotTailPP3.2080.1403.395
TailPP3.1840.1843.376
calcFDR0.5800.0280.607
ccParams0.5800.0160.636
ccPred0.5920.0120.604
ccSummary0.5920.0080.599
ccTrace0.8480.0040.854
histTailPP3.1770.1483.375
plotBasic0.6520.0080.661
plotCompare0.0120.0000.010
plotFDR0.6400.0080.646
plotMixDensity2.0480.0562.107
plotPredChecks0.6600.0080.671
plotTrace0.8320.0160.893