BioC 3.3: CHECK report for BGmix on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:38 -0400 (Tue, 27 Oct 2015).
BGmix 1.31.0 Alex Lewin
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BGmix | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
Summary
Package: BGmix |
Version: 1.31.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.31.0.tar.gz |
StartedAt: 2015-10-27 01:58:13 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 01:59:19 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 65.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BGmix.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BGmix_1.31.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/BGmix.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-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 ‘1.31.0’
* 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 ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
FDRforTailPP 8.247 0.28 8.554
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -DUSING_R -c rundir.cpp -o rundir.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I ../boostIncl -I/usr/local/include -fpic -g -O2 -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
rm -r ../boostIncl
installing to /home/biocbuild/bbs-3.3-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 | 2.967 | 0.064 | 3.031 |
|
BGmix | 4.814 | 0.044 | 4.858 |
|
EstimatePi0 | 3.716 | 0.083 | 3.801 |
|
FDRforTailPP | 8.247 | 0.280 | 8.554 |
|
FDRplotTailPP | 2.970 | 0.072 | 3.042 |
|
TailPP | 2.843 | 0.100 | 2.947 |
|
calcFDR | 0.712 | 0.000 | 0.715 |
|
ccParams | 0.799 | 0.012 | 0.816 |
|
ccPred | 0.798 | 0.004 | 0.804 |
|
ccSummary | 0.783 | 0.012 | 0.797 |
|
ccTrace | 1.097 | 0.012 | 1.110 |
|
histTailPP | 3.480 | 0.088 | 3.573 |
|
plotBasic | 0.644 | 0.004 | 0.647 |
|
plotCompare | 0.008 | 0.000 | 0.009 |
|
plotFDR | 0.556 | 0.004 | 0.560 |
|
plotMixDensity | 1.700 | 0.028 | 1.729 |
|
plotPredChecks | 0.687 | 0.004 | 0.692 |
|
plotTrace | 1.115 | 0.024 | 1.140 |
|