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BioC 3.0: CHECK report for ChIPseqR on moscato1

This page was generated on 2015-04-10 09:46:00 -0700 (Fri, 10 Apr 2015).

Package 151/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.20.0
Peter Humburg
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ChIPseqR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: ChIPseqR
Version: 1.20.0
Command: rm -rf ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && mkdir ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseqR.buildbin-libdir ChIPseqR_1.20.0.tar.gz >ChIPseqR.Rcheck\00install.out 2>&1 && cp ChIPseqR.Rcheck\00install.out ChIPseqR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChIPseqR.buildbin-libdir --install="check:ChIPseqR-install.out" --force-multiarch --no-vignettes --timings ChIPseqR_1.20.0.tar.gz
StartedAt: 2015-04-09 23:38:19 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:47:44 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 565.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPseqR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && mkdir ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseqR.buildbin-libdir ChIPseqR_1.20.0.tar.gz >ChIPseqR.Rcheck\00install.out 2>&1 && cp ChIPseqR.Rcheck\00install.out ChIPseqR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChIPseqR.buildbin-libdir --install="check:ChIPseqR-install.out" --force-multiarch --no-vignettes --timings ChIPseqR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ChIPseqR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.20.0'
* 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 whether package 'ChIPseqR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'graphics::image' when loading 'ChIPseqR'
See 'D:/biocbld/bbs-3.0-bioc/meat/ChIPseqR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'ShortRead'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in 'inst/CITATION':
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument "textVersion" is missing, with no default
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.twoWayTest'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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-3.0-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386/ChIPseqR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64/ChIPseqR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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' ... [94s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
alignFeature       21.11   1.51   22.62
BindScore          16.60   0.14   16.74
RLEBindScore-class 15.24   0.11   15.35
callBindingSites   14.79   0.08   14.86
simpleNucCall      12.62   0.08   12.70
** running examples for arch 'x64' ... [102s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
alignFeature       22.10   1.70   23.81
BindScore          20.64   0.32   20.95
RLEBindScore-class 16.21   0.14   16.36
callBindingSites   13.89   0.17   14.05
simpleNucCall      13.86   0.14   13.99
* 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.

ChIPseqR.Rcheck/00install.out:


install for i386

* installing *source* package 'ChIPseqR' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
gcc -m32 -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'graphics::image' when loading 'ChIPseqR'
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::image' when loading 'ChIPseqR'
No methods found in "IRanges" for requests: sapply

install for x64

* installing *source* package 'ChIPseqR' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::image' when loading 'ChIPseqR'
No methods found in "IRanges" for requests: sapply
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.20.0.zip
* DONE (ChIPseqR)

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

nameusersystemelapsed
BindScore16.60 0.1416.74
ChIPseqR-package000
RLEBindScore-class15.24 0.1115.35
RLEReadCounts-class0.030.000.04
ReadCounts0.060.000.06
alignFeature21.11 1.5122.62
callBindingSites14.79 0.0814.86
pos2gff000
simpleNucCall12.62 0.0812.70
strandPileup000
windowCounts0.060.000.07

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

nameusersystemelapsed
BindScore20.64 0.3220.95
ChIPseqR-package000
RLEBindScore-class16.21 0.1416.36
RLEReadCounts-class0.030.000.03
ReadCounts0.050.000.05
alignFeature22.10 1.7023.81
callBindingSites13.89 0.1714.05
pos2gff0.010.000.02
simpleNucCall13.86 0.1413.99
strandPileup000
windowCounts0.060.000.06