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Package 9/462HostnameOS / ArchBUILDCHECKBUILD BIN
ACME 2.9.0
Sean Davis
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ACME
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ACME
Version: 2.9.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ACME_2.9.0.tar.gz
StartedAt: 2011-05-09 11:10:28 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 11:11:44 -0700 (Mon, 09 May 2011)
EllapsedTime: 76.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ACME.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ACME.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.9.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘ACME’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 33.4Mb
  sub-directories of 1Mb or more:
    extdata  27.3Mb
    data      4.6Mb
    doc       1.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
findClosestGene: no visible binding for global variable ‘refflat’
findClosestGene: no visible binding for '<<-' assignment to ‘refflat’
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... 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

ACME.Rcheck/00install.out:

* installing *source* package ‘ACME’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c windowChisq.c -o windowChisq.o
windowChisq.c: In function ‘windowChisq’:
windowChisq.c:58:4: warning: suggest parentheses around comparison in operand of ‘&’
windowChisq.c:63:4: warning: suggest parentheses around comparison in operand of ‘&’
windowChisq.c:21:11: warning: unused variable ‘xa’
windowChisq.c: At top level:
windowChisq.c:86:5: warning: initialization from incompatible pointer type
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ACME.so windowChisq.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/ACME.Rcheck/ACME/libs
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Creating a new generic function for "print" in "ACME"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘ACME.Rnw’ 
** testing if installed package can be loaded

* DONE (ACME)

ACME.Rcheck/ACME-Ex.timings:

nameusersystemelapsed
ACMECalcSet-class7.3400.1527.501
ACMESet-class0.3680.0000.367
aGFF-class0.3600.0080.368
aGFFCalc-class4.3320.0644.412
do.aGFF.calc4.0850.0204.171
example.agff0.3760.0000.406
findClosestGene1.8040.0285.245
findRegions6.5840.0406.824
generics0.3320.0040.334
getRefflat1.8640.0284.738
read.resultsGFF6.1890.0286.308
write.sgr1.7680.0281.819