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Package 304/419HostnameOS / ArchBUILDCHECKBUILD BIN
PICS 1.4.0
Arnaud Droit , Xuekui Zhang , Raphael Gottardo
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/PICS
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: PICS
Version: 1.4.0
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings PICS_1.4.0.tar.gz
StartedAt: 2011-03-31 09:52:47 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 09:55:16 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 148.6 seconds
RetCode: 0
Status:  OK  
CheckDir: PICS.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/PICS.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PICS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PICS' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'PICS' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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
PICS: no visible global function definition for 'mclapply'
* 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 line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

PICS.Rcheck/00install.out:

* installing *source* package 'PICS' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include        -O2 -Wall  -std=gnu99 -c background.c -o background.o
background.c: In function 'background':
background.c:44:9: warning: statement with no effect
background.c:97:9: warning: statement with no effect
background.c:12:10: warning: unused variable 'length'
background.c:10:26: warning: unused variable 'countR'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include        -O2 -Wall  -std=gnu99 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:804:3: warning: suggest parentheses around comparison in operand of '&'
pics.c:964:3: warning: suggest parentheses around comparison in operand of '&'
pics.c:652:15: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010:66: warning: unused variable 'ee'
pics.c:1010:57: warning: unused variable 'ggR'
pics.c:1010:52: warning: unused variable 'ggF'
pics.c:1010:47: warning: unused variable 'aaR'
pics.c:1010:42: warning: unused variable 'aaF'
pics.c:1010:29: warning: unused variable 'etaDiff'
pics.c:1001:15: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273:96: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634:76: warning: unused variable 'PhiRw'
pics.c:1634:69: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890:11: warning: unused variable 'j'
pics.c:1890:7: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276:35: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421:7: warning: 'ans' may be used uninitialized in this function
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include        -O2 -Wall  -std=gnu99 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106:3: warning: suggest parentheses around comparison in operand of '&'
segment.c:97:45: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:248:7: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284:11: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461:9: warning: suggest parentheses around comparison in operand of '&'
segment.c:1462:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1463:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1464:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1465:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1466:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1467:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1409:8: warning: unused variable 'filter1'
segment.c:1408:11: warning: unused variable 'muFilter'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o PICS.dll tmp.def background.o pics.o segment.o -lws2_32 -LC:/Rtools212/GSL64/lib -lgsl -lgslcblas -lm -LD:/biocbld/BBS-2˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/PICS.Rcheck/PICS/libs/x64
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

Loading required package: Biostrings
in method for 'as.list' with signature '"AlignedRead"': no definition for class "AlignedRead"
in method for 'coerce' with signature '"AlignedRead","GenomeData"': no definition for class "AlignedRead"
Creating a new generic function for "density" in "PICS"
Creating a new generic function for "plot" in "PICS"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (PICS)

PICS.Rcheck/PICS-Ex.timings:

nameusersystemelapsed
makeRangedDataOutput000
pics-class000
picsError-class000
picsFDR000
picsList-class000
segmentReads3.530.003.53
setParaEM000
setParaPrior000