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BioC 3.2: CHECK report for ACME on perceval

This page was generated on 2015-10-27 17:33:27 -0400 (Tue, 27 Oct 2015).

Package 12/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACME 2.26.0
Sean Davis
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ACME
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ACME
Version: 2.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ACME_2.26.0.tar.gz
StartedAt: 2015-10-27 04:38:21 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:14:23 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 2162.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ACME.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ACME_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ACME.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘2.26.0’
* 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 ... [0m/29m] OK
* checking installed package size ... NOTE
  installed size is 44.5Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    extdata  41.0Mb
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/102s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
getRefflat        5.264  0.103  15.248
findClosestGene   5.234  0.106  12.058
read.resultsGFF   5.128  0.209  11.251
findRegions       5.138  0.163   5.301
ACMECalcSet-class 3.391  0.158   6.730
write.sgr         3.193  0.186  15.027
write.bedGraph    2.124  0.111  26.196
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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/Library/Frameworks/R.framework/Resources/lib -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-3.2-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-class3.3910.1586.730
ACMESet-class0.5950.0210.616
aGFF-class0.6090.0120.622
aGFFCalc-class2.8230.0952.918
do.aGFF.calc2.7940.1572.951
example.agff0.7680.0360.805
findClosestGene 5.234 0.10612.058
findRegions5.1380.1635.301
generics0.5660.0200.587
getRefflat 5.264 0.10315.248
read.resultsGFF 5.128 0.20911.251
write.bedGraph 2.124 0.11126.196
write.sgr 3.193 0.18615.027