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BioC 2.13: CHECK report for ACME on perceval

This page was generated on 2014-04-05 09:51:56 -0700 (Sat, 05 Apr 2014).

Package 9/750HostnameOS / ArchBUILDCHECKBUILD BIN
ACME 2.18.0
Sean Davis
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/ACME
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: ACME
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ACME_2.18.0.tar.gz
StartedAt: 2014-04-04 23:08:44 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:10:47 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 122.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ACME.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ACME.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 ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.18.0’
* 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 ‘ACME’ can be installed ... [5s/6s] OK
* checking installed package size ... NOTE
  installed size is 30.9Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    extdata  27.3Mb
* 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 ... 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 compiled code ... OK
* 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’:
  ‘ACME.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [61s/65s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ACMECalcSet-class 9.685  0.433  10.537
findRegions       9.160  0.817  10.063
read.resultsGFF   7.253  0.527   7.885
aGFFCalc-class    5.708  0.608   6.607
do.aGFF.calc      5.454  0.661   6.322
getRefflat        5.690  0.220   6.930
findClosestGene   5.286  0.248   6.561
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/ACME.Rcheck/00check.log’
for details.

ACME.Rcheck/00install.out:

* installing *source* package ‘ACME’ ...
** 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 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
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 ACME.so windowChisq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/ACME.Rcheck/ACME/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘ACME’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ACME)

ACME.Rcheck/ACME-Ex.timings:

nameusersystemelapsed
ACMECalcSet-class 9.685 0.43310.537
ACMESet-class0.5550.0680.685
aGFF-class0.5170.0530.639
aGFFCalc-class5.7080.6086.607
do.aGFF.calc5.4540.6616.322
example.agff0.5420.0670.622
findClosestGene5.2860.2486.561
findRegions 9.160 0.81710.063
generics0.5140.0400.564
getRefflat5.690.226.93
read.resultsGFF7.2530.5277.885
write.bedGraph2.2750.2442.665
write.sgr2.0380.2032.734