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Package 368/609HostnameOS / ArchBUILDCHECKBUILD BIN
MEDIPS 1.8.0
Lukas Chavez
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/MEDIPS
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: MEDIPS
Version: 1.8.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.8.0.tar.gz
StartedAt: 2013-03-25 02:52:45 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:01:17 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 512.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.8.0’
* 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 47.8Mb
  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 for left-over 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.CpGenrich            98.850  4.876 106.523
MEDIPS.selectSignificants  102.367  1.092 105.017
MEDIPS.saturationAnalysis   42.042  0.036  43.002
MEDIPS.plotSaturation       40.594  0.032  41.018
MEDIPS.plotCoverage         10.081  0.072  10.180
MEDIPS.coverageAnalysis      9.080  0.036   9.212
MEDIPS.methylProfiling       8.772  0.064   9.067
MEDIPS.plotCalibrationPlot   8.172  0.128   8.839
MEDIPS.normalize             6.225  0.040   6.381
MEDIPS.calibrationCurve      5.128  0.468   5.634
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.

MEDIPS.Rcheck/00install.out:

* installing *source* package ‘MEDIPS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:21:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
annotate.c:32:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
annotate.c:43:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
annotate.c:8:40: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
annotate.c:8:32: warning: unused variable ‘rj’ [-Wunused-variable]
annotate.c:8:25: warning: variable ‘ac’ set but not used [-Wunused-but-set-variable]
annotate.c:8:17: warning: unused variable ‘aj’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c calibration.c -o calibration.o
calibration.c: In function ‘calibration’:
calibration.c:10:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c coupling.c -o coupling.o
coupling.c: In function ‘coupling’:
coupling.c:26:9: warning: statement with no effect [-Wunused-value]
coupling.c:8:9: warning: variable ‘score’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c profile.c -o profile.o
profile.c: In function ‘profile’:
profile.c:42:15: warning: unused variable ‘wie’ [-Wunused-variable]
profile.c:221:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:221:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:221:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:221:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:227:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:227:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:227:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:227:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:263:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:263:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:263:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:263:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:269:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:269:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:269:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:269:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
profile.c:34:9: warning: unused variable ‘items’ [-Wunused-variable]
profile.c:13:13: warning: variable ‘ptrgenome’ set but not used [-Wunused-but-set-variable]
profile.c:11:22: warning: unused variable ‘pvalue’ [-Wunused-variable]
profile.c:11:18: warning: unused variable ‘Val’ [-Wunused-variable]
profile.c:246:21: warning: ‘nY’ may be used uninitialized in this function [-Wuninitialized]
profile.c:274:8: warning: ‘Y’ may be used uninitialized in this function [-Wuninitialized]
profile.c:7:6: warning: ‘ptr_input’ may be used uninitialized in this function [-Wuninitialized]
profile.c:7:6: warning: ‘ptrgenome_norm2’ may be used uninitialized in this function [-Wuninitialized]
profile.c:7:6: warning: ‘ptrgenome_raw2’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c roiprofile.c -o roiprofile.o
roiprofile.c: In function ‘calculate’:
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:181:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:186:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:221:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:226:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:23:28: warning: variable ‘ptrgenome_pos’ set but not used [-Wunused-but-set-variable]
roiprofile.c:12:18: warning: unused variable ‘Val’ [-Wunused-variable]
roiprofile.c: In function ‘roiprofile’:
roiprofile.c:280:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:282:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:294:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:296:6: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
roiprofile.c:254:27: warning: variable ‘ncol’ set but not used [-Wunused-but-set-variable]
roiprofile.c:248:62: warning: unused variable ‘nProtected’ [-Wunused-variable]
roiprofile.c: In function ‘calculate’:
roiprofile.c:7:6: warning: ‘ptrinput’ may be used uninitialized in this function [-Wuninitialized]
roiprofile.c:69:31: warning: ‘IN’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck/MEDIPS/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘MEDIPS.Rnw’ 
** testing if installed package can be loaded

* DONE (MEDIPS)

MEDIPS.Rcheck/MEDIPS-Ex.timings:

nameusersystemelapsed
MEDIPS.CpGenrich 98.850 4.876106.523
MEDIPS.annotate0.0280.0000.028
MEDIPS.calibrationCurve5.1280.4685.634
MEDIPS.couplingVector3.9810.1004.128
MEDIPS.coverageAnalysis9.0800.0369.212
MEDIPS.exportWIG4.6440.0404.716
MEDIPS.genomeVector3.1930.0283.224
MEDIPS.getPositions2.0240.0282.059
MEDIPS.mergeFrames0.0040.0000.006
MEDIPS.methylProfiling8.7720.0649.067
MEDIPS.normalize6.2250.0406.381
MEDIPS.plotCalibrationPlot8.1720.1288.839
MEDIPS.plotCoverage10.081 0.07210.180
MEDIPS.plotSaturation40.594 0.03241.018
MEDIPS.readAlignedSequences1.5810.0201.623
MEDIPS.saturationAnalysis42.042 0.03643.002
MEDIPS.selectSignificants102.367 1.092105.017
MEDIPSset-class0.0000.0000.002