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Package 280/462HostnameOS / ArchBUILDCHECKBUILD BIN
MEDIPS 1.3.0
Lukas Chavez
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEDIPS
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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: 1.3.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings MEDIPS_1.3.0.tar.gz
StartedAt: 2011-05-09 14:31:49 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:40:54 -0700 (Mon, 09 May 2011)
EllapsedTime: 545.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/MEDIPS.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.3.0'
* 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 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 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 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

MEDIPS.Rcheck/00install.out:

* installing *source* package 'MEDIPS' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:21:10: warning: suggest parentheses around comparison in operand of '&'
annotate.c:32:4: warning: suggest parentheses around comparison in operand of '&'
annotate.c:43:4: warning: suggest parentheses around comparison in operand of '&'
annotate.c:8:32: warning: unused variable 'rj'
annotate.c:8:17: warning: unused variable 'aj'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c calibration.c -o calibration.o
calibration.c: In function 'calibration':
calibration.c:10:6: warning: suggest parentheses around comparison in operand of '&'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c coupling.c -o coupling.o
coupling.c: In function 'coupling':
coupling.c:26:9: warning: statement with no effect
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c profile.c -o profile.o
profile.c: In function 'profile':
profile.c:42:15: warning: unused variable 'wie'
profile.c:221:14: warning: suggest parentheses around comparison in operand of '&'
profile.c:221:14: warning: suggest parentheses around comparison in operand of '&'
profile.c:221:14: warning: suggest parentheses around comparison in operand of '&'
profile.c:221:14: warning: suggest parentheses around comparison in operand of '&'
profile.c:227:20: warning: suggest parentheses around comparison in operand of '&'
profile.c:227:20: warning: suggest parentheses around comparison in operand of '&'
profile.c:227:20: warning: suggest parentheses around comparison in operand of '&'
profile.c:227:20: warning: suggest parentheses around comparison in operand of '&'
profile.c:263:17: warning: suggest parentheses around comparison in operand of '&'
profile.c:263:17: warning: suggest parentheses around comparison in operand of '&'
profile.c:263:17: warning: suggest parentheses around comparison in operand of '&'
profile.c:263:17: warning: suggest parentheses around comparison in operand of '&'
profile.c:269:11: warning: suggest parentheses around comparison in operand of '&'
profile.c:269:11: warning: suggest parentheses around comparison in operand of '&'
profile.c:269:11: warning: suggest parentheses around comparison in operand of '&'
profile.c:269:11: warning: suggest parentheses around comparison in operand of '&'
profile.c:34:9: warning: unused variable 'items'
profile.c:11:22: warning: unused variable 'pvalue'
profile.c:11:18: warning: unused variable 'Val'
profile.c:25:13: warning: 'ptrgenome_raw2' may be used uninitialized in this function
profile.c:25:29: warning: 'ptrgenome_norm2' may be used uninitialized in this function
profile.c:13:96: warning: 'ptr_input' may be used uninitialized in this function
profile.c:11:39: warning: 'Y' may be used uninitialized in this function
profile.c:11:44: warning: 'nY' may be used uninitialized in this function
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c roiprofile.c -o roiprofile.o
roiprofile.c: In function 'calculate':
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:12:18: warning: unused variable 'Val'
roiprofile.c: In function 'roiprofile':
roiprofile.c:280:7: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:282:13: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:294:6: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:296:6: warning: suggest parentheses around comparison in operand of '&'
roiprofile.c:248:62: warning: unused variable 'nProtected'
roiprofile.c: In function 'calculate':
roiprofile.c:29:10: warning: 'IN' may be used uninitialized in this function
roiprofile.c:29:21: warning: 'ptrinput' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o MEDIPS.dll tmp.def annotate.o calibration.o coupling.o profile.o roiprofile.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-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, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'MEDIPS.Rnw' 
** testing if installed package can be loaded

* DONE (MEDIPS)

MEDIPS.Rcheck/MEDIPS-Ex.timings:

nameusersystemelapsed
MEDIPS.CpGenrich 92.75 4.27109.22
MEDIPS.annotate0.030.000.03
MEDIPS.calibrationCurve6.380.416.83
MEDIPS.couplingVector5.310.285.61
MEDIPS.coverageAnalysis10.30 0.8611.31
MEDIPS.exportWIG7.790.118.12
MEDIPS.genomeVector4.390.224.66
MEDIPS.getPositions3.380.073.47
MEDIPS.mergeFrames000
MEDIPS.methylProfiling9.440.399.92
MEDIPS.normalize6.770.437.20
MEDIPS.plotCalibrationPlot13.91 0.4614.52
MEDIPS.plotCoverage11.09 0.6111.77
MEDIPS.plotSaturation50.13 0.2750.59
MEDIPS.readAlignedSequences3.010.113.19
MEDIPS.saturationAnalysis49.57 0.2550.03
MEDIPS.selectSignificants121.97 1.53124.77
MEDIPSset-class000