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BioC 2.14: CHECK report for ACME on morelia

This page was generated on 2014-10-08 09:03:08 -0700 (Wed, 08 Oct 2014).

Package 10/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACME 2.20.0
Sean Davis
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ACME
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: ACME
Version: 2.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ACME_2.20.0.tar.gz
StartedAt: 2014-10-07 20:59:57 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:01:26 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 88.9 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 --no-multiarch ACME_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ACME.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.20.0’
* 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 ... [4s/4s] 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... [43s/46s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
read.resultsGFF   9.390  0.154   9.566
findRegions       6.295  0.144   6.445
ACMECalcSet-class 4.933  0.120   5.056
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/ACME.Rcheck/00check.log’
for details.

ACME.Rcheck/00install.out:

* installing *source* package ‘ACME’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c windowChisq.c -o windowChisq.o
windowChisq.c:57:71: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
    while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
                                                                      ^
windowChisq.c:57:71: note: place parentheses around the '>' expression to silence this warning
    while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
                                                                      ^
windowChisq.c:57:71: note: place parentheses around the & expression to evaluate it first
    while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
                                                                      ^
windowChisq.c:62:70: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
    while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
                                                                     ^
windowChisq.c:62:70: note: place parentheses around the '<' expression to silence this warning
    while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
                                                                     ^
windowChisq.c:62:70: note: place parentheses around the & expression to evaluate it first
    while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
                                                                     ^
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
  double *xa,*xlocations,*xchivals;
          ^
windowChisq.c:86:20: warning: incompatible pointer types initializing 'DL_FUNC' (aka 'void *(*)()') with an expression of type 'SEXP (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' [-Wincompatible-pointer-types]
    {"windowChisq",&windowChisq,5},
                   ^˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -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-2.14-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-class4.9330.1205.056
ACMESet-class0.6540.0350.689
aGFF-class0.5530.0160.569
aGFFCalc-class3.6840.1013.787
do.aGFF.calc3.5650.1223.688
example.agff0.7050.0270.733
findClosestGene2.9590.0733.823
findRegions6.2950.1446.445
generics0.5470.0190.568
getRefflat3.1310.0694.501
read.resultsGFF9.3900.1549.566
write.bedGraph2.5610.1152.858
write.sgr2.0340.0732.111