BioC 2.9: CHECK report for MEDIPS on pitt

Package: MEDIPS

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.4.0.tar.gz

StartedAt: 2012-03-24 02:27:28 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:40:00 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 752.7 seconds

RetCode: 0

Status: OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/MEDIPS.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.4.0'
* 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 whether package 'MEDIPS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 47.7Mb
  sub-directories of 1Mb or more:
    extdata  47.0Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'MEDIPS' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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-2.9-bioc/meat/MEDIPS.Rcheck/MEDIPS/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'MEDIPS.Rnw' 
** testing if installed package can be loaded

* DONE (MEDIPS)

name	user	system	elapsed
MEDIPS.CpGenrich	182.186	18.961	210.833
MEDIPS.annotate	0.052	0.005	0.057
MEDIPS.calibrationCurve	7.301	1.892	9.508
MEDIPS.couplingVector	6.151	1.468	7.984
MEDIPS.coverageAnalysis	14.024	4.496	19.484
MEDIPS.exportWIG	6.972	1.394	8.612
MEDIPS.genomeVector	4.393	1.027	5.500
MEDIPS.getPositions	3.338	0.511	3.886
MEDIPS.mergeFrames	0.006	0.000	0.006
MEDIPS.methylProfiling	10.606	2.304	13.075
MEDIPS.normalize	8.038	2.091	10.270
MEDIPS.plotCalibrationPlot	10.580	1.978	12.795
MEDIPS.plotCoverage	16.045	4.426	20.683
MEDIPS.plotSaturation	59.063	2.043	61.502
MEDIPS.readAlignedSequences	2.511	0.321	2.855
MEDIPS.saturationAnalysis	59.881	2.127	63.699
MEDIPS.selectSignificants	133.912	8.463	146.449
MEDIPSset-class	0.001	0.001	0.003

Summary

Command output