BioC 2.13: CHECK report for methylMnM on perceval
This page was generated on 2014-04-05 09:53:16 -0700 (Sat, 05 Apr 2014).
methylMnM 1.0.0 Yan Zhou
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/methylMnM | 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: methylMnM |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methylMnM_1.0.0.tar.gz |
StartedAt: 2014-04-05 02:33:09 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 02:34:30 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 80.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylMnM.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/methylMnM.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylMnM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylMnM’ version ‘1.0.0’
* 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 ‘methylMnM’ can be installed ... [5s/7s] OK
* checking installed package size ... NOTE
installed size is 47.8Mb
sub-directories of 1Mb or more:
extdata 47.4Mb
* 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’ calls to packages already attached by Depends:
‘edgeR’ ‘statmod’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘edgeR’ ‘statmod’
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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/methylMnM.Rcheck/methylMnM/libs/methylMnM.so’:
Found ‘_printf’, possibly from ‘printf’ (C)
Objects: ‘CpGcount.o’, ‘calculatecount.o’, ‘calculatecount1.o’,
‘calculatecountneg.o’, ‘pmultinom.o’, ‘pvalueclassify.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘methylMnM.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [18s/21s] OK
* 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
‘/Users/biocbuild/bbs-2.13-bioc/meat/methylMnM.Rcheck/00check.log’
for details.
methylMnM.Rcheck/00install.out:
* installing *source* package ‘methylMnM’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c CpGcount.c -o CpGcount.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c calculatecount.c -o calculatecount.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c calculatecount1.c -o calculatecount1.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c calculatecountneg.c -o calculatecountneg.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c pmultinom.c -o pmultinom.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c pvalueclassify.c -o pvalueclassify.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c register.c -o register.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o methylMnM.so CpGcount.o calculatecount.o calculatecount1.o calculatecountneg.o pmultinom.o pvalueclassify.o register.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/methylMnM.Rcheck/methylMnM/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 (methylMnM)
methylMnM.Rcheck/methylMnM-Ex.timings:
name | user | system | elapsed
|
CNVnormal | 0.048 | 0.004 | 0.067 |
|
MnM.qvalue | 0.052 | 0.004 | 0.056 |
|
MnM.selectDMR | 0.029 | 0.001 | 0.031 |
|
MnM.test | 0.144 | 0.005 | 0.151 |
|
calcFactornew | 0.013 | 0.000 | 0.015 |
|
calculatecount | 0.009 | 0.001 | 0.009 |
|
calculatecount1 | 0.007 | 0.000 | 0.007 |
|
calculatecountneg | 0.009 | 0.000 | 0.009 |
|
countMREbin | 4.227 | 0.191 | 4.890 |
|
countMREcpgbin | 3.620 | 0.255 | 4.692 |
|
countMeDIPbin | 2.371 | 0.226 | 3.084 |
|
countcpgbin | 2.577 | 0.207 | 3.189 |
|
cpgcount | 0.011 | 0.009 | 0.021 |
|
normpdf | 0.010 | 0.008 | 0.018 |
|
normpdf1 | 0.010 | 0.008 | 0.020 |
|
pmultinom | 2.167 | 0.014 | 2.368 |
|
qvalue.rank | 0.002 | 0.004 | 0.007 |
|
removeblacklist | 0.019 | 0.012 | 0.040 |
|