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BioC 2.12: CHECK report for metahdep on george2

This page was generated on 2013-10-09 09:37:32 -0700 (Wed, 09 Oct 2013).

Package 404/671HostnameOS / ArchBUILDCHECKBUILD BIN
metahdep 1.18.0
John R. Stevens
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/metahdep
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: metahdep
Version: 1.18.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings metahdep_1.18.0.tar.gz
StartedAt: 2013-10-09 03:10:07 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:11:00 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 52.8 seconds
RetCode: 0
Status:  OK 
CheckDir: metahdep.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/metahdep.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metahdep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metahdep’ version ‘1.18.0’
* 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 ‘metahdep’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... NOTE
prepare_Rd: metahdep.other.Rd:40-42: Dropping empty section \usage
prepare_Rd: metahdep.other.Rd:43-45: Dropping empty section \arguments
prepare_Rd: metahdep.other.Rd:46-48: Dropping empty section \value
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [9s/9s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/metahdep.Rcheck/00check.log’
for details.

metahdep.Rcheck/00install.out:

* installing *source* package ‘metahdep’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c metahdep.c -o metahdep.o
metahdep.c: In function ‘get_row_indices2’:
metahdep.c:471:5: warning: passing argument 5 of ‘metan_binary_search_unique’ makes integer from pointer without a cast [enabled by default]
metahdep.c:372:6: note: expected ‘char’ but argument is of type ‘const char *’
gcc -std=gnu99 -shared -L/usr/local/lib -o metahdep.so metahdep.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/metahdep.Rcheck/metahdep/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 (metahdep)

metahdep.Rcheck/metahdep-Ex.timings:

nameusersystemelapsed
ES.obj-class0.1120.0160.130
HGU.DifExp.list0.0280.0000.031
HGU.newnames0.3560.0080.367
HGU.prep.list0.0760.0120.088
getPLM.es0.0200.0000.021
gloss0.0320.0000.030
metahdep.FEMA0.0880.0120.099
metahdep.HBLM1.7040.0481.757
metahdep3.4280.0323.472
metahdep.REMA0.4200.0080.430
metahdep.format0.6160.0040.624
metahdep.other0.1280.0000.130
metaprep-class0.2640.0000.263