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BioC 3.4: CHECK report for BAC on moscato1

This page was generated on 2016-09-21 03:42:24 -0700 (Wed, 21 Sep 2016).

Package 73/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BAC 1.33.0
Raphael Gottardo
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BAC
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BAC
Version: 1.33.0
Command: rm -rf BAC.buildbin-libdir BAC.Rcheck && mkdir BAC.buildbin-libdir BAC.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BAC.buildbin-libdir BAC_1.33.0.tar.gz >BAC.Rcheck\00install.out 2>&1 && cp BAC.Rcheck\00install.out BAC-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BAC.buildbin-libdir --install="check:BAC-install.out" --force-multiarch --no-vignettes --timings BAC_1.33.0.tar.gz
StartedAt: 2016-09-20 04:10:55 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:15:35 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 279.5 seconds
RetCode: 0
Status:  OK  
CheckDir: BAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BAC.buildbin-libdir BAC.Rcheck && mkdir BAC.buildbin-libdir BAC.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BAC.buildbin-libdir BAC_1.33.0.tar.gz >BAC.Rcheck\00install.out 2>&1 && cp BAC.Rcheck\00install.out BAC-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BAC.buildbin-libdir --install="check:BAC-install.out" --force-multiarch --no-vignettes --timings BAC_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/BAC.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BAC' version '1.33.0'
* 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 whether package 'BAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
BAC: no visible global function definition for 'median'
BAC: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median
Consider adding
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: BAC.Rd:37-38: Dropping empty section \note
prepare_Rd: CallRegions.Rd:21-23: Dropping empty section \details
prepare_Rd: CallRegions.Rd:34-35: Dropping empty section \note
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/BAC.buildbin-libdir/BAC/libs/i386/BAC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
CallRegions 64.10      0   64.12
BAC         63.45      0   63.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
BAC         62.82      0   62.84
CallRegions 61.90      0   61.90
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/BAC.Rcheck/00check.log'
for details.


BAC.Rcheck/00install.out:


install for i386

* installing *source* package 'BAC' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BAC.c -o BAC.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o BAC.dll tmp.def BAC.o util.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/BAC.buildbin-libdir/BAC/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'BAC' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BAC.c -o BAC.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o BAC.dll tmp.def BAC.o util.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/BAC.buildbin-libdir/BAC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BAC' as BAC_1.33.0.zip
* DONE (BAC)

BAC.Rcheck/examples_i386/BAC-Ex.timings:

nameusersystemelapsed
BAC63.45 0.0063.45
CallRegions64.10 0.0064.12

BAC.Rcheck/examples_x64/BAC-Ex.timings:

nameusersystemelapsed
BAC62.82 0.0062.84
CallRegions61.9 0.061.9