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Package 9/467HostnameOS / ArchBUILDCHECKBUILD BIN
ACME 2.8.0
Sean Davis
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/ACME
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: ACME
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ACME_2.8.0.tar.gz
StartedAt: 2011-10-20 13:04:37 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 13:06:20 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 102.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ACME.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ACME.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '2.8.0'
* checking package namespace 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 33.3Mb
  sub-directories of 1Mb or more:
    data      4.6Mb
    doc       1.3Mb
    extdata  27.3Mb
* 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 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 ... 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'ACME.pdf' from 1291Kb to 201Kb
  consider running tools::compactPDF() on these files
* 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c windowChisq.c -o windowChisq.o
windowChisq.c: In function 'windowChisq':
windowChisq.c:58: warning: suggest parentheses around comparison in operand of &
windowChisq.c:63: warning: suggest parentheses around comparison in operand of &
windowChisq.c:21: warning: unused variable 'xa'
windowChisq.c: At top level:
windowChisq.c:86: warning: initialization from incompatible pointer type
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ACME.so windowChisq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/ACME.Rcheck/ACME/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "print" in "ACME"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ACME)

ACME.Rcheck/ACME-Ex.timings:

nameusersystemelapsed
ACMECalcSet-class6.7930.9147.840
ACMESet-class0.7750.0240.807
aGFF-class0.7780.0290.814
aGFFCalc-class4.9760.8925.965
do.aGFF.calc4.6300.8795.556
example.agff0.7880.0290.829
findClosestGene4.0470.1875.074
findRegions7.8441.2219.242
generics0.7710.0260.822
getRefflat3.7200.1604.481
read.resultsGFF7.3950.7678.611
write.sgr2.7730.2733.192