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 |
* 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.
* 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)