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BioC 2.13: CHECK report for BGmix on zin1

This page was generated on 2014-04-05 09:47:34 -0700 (Sat, 05 Apr 2014).

Package 70/750HostnameOS / ArchBUILDCHECKBUILD BIN
BGmix 1.22.0
Alex Lewin
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/BGmix
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 N O T   S U P P O R T E D
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: BGmix
Version: 1.22.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.22.0.tar.gz
StartedAt: 2014-04-04 23:46:40 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:47:41 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 60.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BGmix.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/BGmix.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 ‘BGmix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BGmix’ version ‘1.22.0’
* 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 ... [8s/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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘KernSmooth’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘KernSmooth’
  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 ... NOTE
ccSummary: warning in agrep("genes", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("conds", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("effects", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix comps", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("variance", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix prior", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("niter", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("nburn", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("nthin", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("seed", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("move", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("fullBayes", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("aa updated", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta updated", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambdas updated", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("tau's", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("t-dist", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("(params)", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("(predictive)", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_up", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_down", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda+ for", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda- for", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
plotFDR: warning in legend(xx, yy, leg = c("FDR=5%", "FDR=10%"), col =
  c("red", "blue"), lty = c(1, 1), bg = "white"): partial argument
  match of 'leg' to 'legend'
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/BGmix.Rcheck/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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘BGmix.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
FDRforTailPP 7.789  0.480   8.575
BGmix        5.252  0.048   5.360
* 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 6 notes.
See
  ‘/home/biocbuild/bbs-2.13-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-2.13-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-2.13-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-2.13-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:992:41: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1005:46: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1005:67: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:1015:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
updates_BGmix.cpp:986:5: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
g++ -shared -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
rm -r ../boostIncl 
installing to /home/biocbuild/bbs-2.13-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-package2.4240.0162.450
BGmix5.2520.0485.360
EstimatePi03.3760.1843.583
FDRforTailPP7.7890.4808.575
FDRplotTailPP3.1480.2283.414
TailPP3.0200.2123.250
calcFDR0.5880.0080.607
ccParams0.6600.0040.726
ccPred0.5960.0080.610
ccSummary0.5760.0120.593
ccTrace0.8040.0160.821
histTailPP3.0840.1923.515
plotBasic0.6050.0160.620
plotCompare0.0080.0000.010
plotFDR0.6000.0040.612
plotMixDensity2.0160.0162.099
plotPredChecks0.5880.0240.610
plotTrace0.8160.0040.819