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BioC 3.1: CHECK report for metaArray on petty

This page was generated on 2015-10-09 09:32:57 -0700 (Fri, 09 Oct 2015).

Package 577/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaArray 1.46.0
Hyungwon Choi
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/metaArray
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metaArray
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaArray_1.46.0.tar.gz
StartedAt: 2015-10-09 00:10:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:11:42 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 62.3 seconds
RetCode: 0
Status:  OK 
CheckDir: metaArray.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaArray_1.46.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/metaArray.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaArray/DESCRIPTION’ ... OK
* this is package ‘metaArray’ version ‘1.46.0’
* 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 ‘metaArray’ can be installed ... [6s/8s] 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 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 ... NOTE
poe.mcmc: no visible binding for global variable ‘R0’
* checking Rd files ... NOTE
prepare_Rd: em.draw.Rd:28-30: Dropping empty section \examples
prepare_Rd: find.init.Rd:20-21: Dropping empty section \examples
prepare_Rd: fit.em.Rd:31-33: Dropping empty section \examples
prepare_Rd: poe.em.Rd:22: Dropping empty section \examples
* 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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘metaArray/libs/metaArray.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘perm.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/2s] 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
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/metaArray.Rcheck/00check.log’
for details.


metaArray.Rcheck/00install.out:

* installing *source* package ‘metaArray’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c contr.c -o contr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c dproc.c -o dproc.o
dproc.c: In function ‘free_CH’:
dproc.c:192: warning: unused variable ‘nc’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c dproc2.c -o dproc2.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c intcor.c -o intcor.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c lowess.c -o lowess.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c mmath.c -o mmath.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c perm.c -o perm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DUSEDOUBLE -fPIC  -mtune=core2 -g -O2 -Wall  -c poe.c -o poe.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o metaArray.so contr.o dproc.o dproc2.o intcor.o lowess.o mmath.o perm.o poe.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/metaArray.Rcheck/metaArray/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 (metaArray)

metaArray.Rcheck/metaArray-Ex.timings:

nameusersystemelapsed
Zscore0.0010.0000.000
intcor0.0010.0000.001
poe.mcmc0.0010.0000.001