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This page was generated on 2014-10-08 08:48:19 -0700 (Wed, 08 Oct 2014).
| Package 76/824 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||
| BGmix 1.24.0 Alex Lewin
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... | ||||||||
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |||||
| Package: BGmix |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.24.0.tar.gz |
| StartedAt: 2014-10-07 22:00:14 -0700 (Tue, 07 Oct 2014) |
| EndedAt: 2014-10-07 22:01:14 -0700 (Tue, 07 Oct 2014) |
| EllapsedTime: 60.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BGmix.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/BGmix.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.24.0’
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.14-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 files in ‘vignettes’ ... OK
* checking examples ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
FDRforTailPP 7.873 0.464 8.391
BGmix 5.620 0.068 5.713
* 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 3 notes.
See
‘/home/biocbuild/bbs-2.14-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-2.14-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-2.14-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-2.14-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/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR rm -r ../boostIncl installing to /home/biocbuild/bbs-2.14-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:
| name | user | system | elapsed | |
| BGmix-package | 2.400 | 0.028 | 2.471 | |
| BGmix | 5.620 | 0.068 | 5.713 | |
| EstimatePi0 | 3.280 | 0.136 | 3.424 | |
| FDRforTailPP | 7.873 | 0.464 | 8.391 | |
| FDRplotTailPP | 3.096 | 0.180 | 3.281 | |
| TailPP | 3.044 | 0.152 | 3.201 | |
| calcFDR | 0.616 | 0.012 | 0.632 | |
| ccParams | 0.608 | 0.016 | 0.928 | |
| ccPred | 0.600 | 0.020 | 0.654 | |
| ccSummary | 0.668 | 0.052 | 0.724 | |
| ccTrace | 0.800 | 0.008 | 0.810 | |
| histTailPP | 3.213 | 0.132 | 3.368 | |
| plotBasic | 0.660 | 0.012 | 0.669 | |
| plotCompare | 0.008 | 0.000 | 0.009 | |
| plotFDR | 0.612 | 0.016 | 0.629 | |
| plotMixDensity | 2.132 | 0.052 | 2.185 | |
| plotPredChecks | 0.656 | 0.012 | 0.668 | |
| plotTrace | 0.984 | 0.036 | 1.071 | |