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Package 253/419HostnameOS / ArchBUILDCHECKBUILD BIN
MEDIPS 1.0.0
Lukas Chavez
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/MEDIPS
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: MEDIPS
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.0.0.tar.gz
StartedAt: 2011-03-31 06:44:33 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:58:04 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 810.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/MEDIPS.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDIPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDIPS’ version ‘1.0.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘MEDIPS’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 line endings in Makefiles ... 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

MEDIPS.Rcheck/00install.out:

* installing *source* package ‘MEDIPS’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:21: warning: suggest parentheses around comparison in operand of &
annotate.c:32: warning: suggest parentheses around comparison in operand of &
annotate.c:43: warning: suggest parentheses around comparison in operand of &
annotate.c:8: warning: unused variable ‘rj’
annotate.c:8: warning: unused variable ‘aj’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c calibration.c -o calibration.o
calibration.c: In function ‘calibration’:
calibration.c:10: warning: suggest parentheses around comparison in operand of &
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c coupling.c -o coupling.o
coupling.c: In function ‘coupling’:
coupling.c:26: warning: statement with no effect
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c profile.c -o profile.o
profile.c: In function ‘profile’:
profile.c:42: warning: unused variable ‘wie’
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:34: warning: unused variable ‘items’
profile.c:11: warning: unused variable ‘pvalue’
profile.c:11: warning: unused variable ‘Val’
profile.c:25: warning: ‘ptrgenome_norm2’ may be used uninitialized in this function
profile.c:25: warning: ‘ptrgenome_raw2’ may be used uninitialized in this function
profile.c:13: warning: ‘ptr_input’ may be used uninitialized in this function
profile.c:11: warning: ‘nY’ may be used uninitialized in this function
profile.c:11: warning: ‘Y’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c roiprofile.c -o roiprofile.o
roiprofile.c: In function ‘calculate’:
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:12: warning: unused variable ‘Val’
roiprofile.c: In function ‘roiprofile’:
roiprofile.c:280: warning: suggest parentheses around comparison in operand of &
roiprofile.c:282: warning: suggest parentheses around comparison in operand of &
roiprofile.c:294: warning: suggest parentheses around comparison in operand of &
roiprofile.c:296: warning: suggest parentheses around comparison in operand of &
roiprofile.c:248: warning: unused variable ‘nProtected’
roiprofile.c: In function ‘calculate’:
roiprofile.c:29: warning: ‘ptrinput’ may be used uninitialized in this function
roiprofile.c:29: warning: ‘IN’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/MEDIPS.Rcheck/MEDIPS/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges

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: GenomicRanges
Loading required package: Biostrings
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (MEDIPS)

MEDIPS.Rcheck/MEDIPS-Ex.timings:

nameusersystemelapsed
MEDIPS.CpGenrich179.425 18.576208.851
MEDIPS.annotate0.0480.0020.052
MEDIPS.calibrationCurve6.9891.7859.317
MEDIPS.couplingVector6.0181.4808.154
MEDIPS.coverageAnalysis13.792 4.42719.517
MEDIPS.exportWIG6.8591.2888.812
MEDIPS.genomeVector4.2771.0315.445
MEDIPS.getPositions3.1960.4793.734
MEDIPS.mergeFrames0.0070.0000.007
MEDIPS.methylProfiling10.739 2.35913.389
MEDIPS.normalize 7.959 2.07810.173
MEDIPS.plotCalibrationPlot11.315 2.13313.810
MEDIPS.plotCoverage15.486 4.30521.582
MEDIPS.plotSaturation68.768 2.08272.410
MEDIPS.readAlignedSequences2.6000.3382.982
MEDIPS.saturationAnalysis69.289 2.09272.647
MEDIPS.selectSignificants167.962 7.830182.128
MEDIPSset-class0.0050.0010.006