PING 1.1.0
Xuekui Zhang
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PING | | Last Changed Rev: 64680 / Revision: 66885 | | Last Changed Date: 2012-03-30 15:15:56 -0700 (Fri, 30 Mar 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/PING.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'PING/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PING' version '1.1.0'
* 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 'PING' can be installed ... OK
* checking installed package size ... 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 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 ... NOTE
Found the following possibly unsafe calls:
File 'R/setParaEM.R':
found unlockBinding("paraEMTF", environment(PING))
found unlockBinding("paraEMH", environment(PING))
File 'R/setParaPrior.R':
found unlockBinding("paraPriorTF", environment(PING))
found unlockBinding("paraPriorH", environment(PING))
File 'R/setParaSeg.R':
found unlockBinding("paraSegTF", environment(PING))
found unlockBinding("paraSegH", environment(PING))
truncateResult: warning in read.table(chr.info.name, colClass =
c("character", "integer")): partial argument match of 'colClass' to
'colClasses'
* 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 compilation flags in Makevars ... 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 installed files from 'inst/doc' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
* 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
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/PING.Rcheck/00check.log'
for details.
* installing *source* package 'PING' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'background':
background.c:44: warning: statement with no effect
background.c:97: warning: statement with no effect
background.c:12: warning: unused variable 'length'
background.c:10: warning: unused variable 'countR'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:142: warning: suggest parentheses around comparison in operand of &
ping.c: In function 'iterEM':
ping.c:637: warning: unused variable 'mu'
ping.c: In function 'ECM1':
ping.c:882: warning: suggest parentheses around comparison in operand of &
ping.c:1042: warning: suggest parentheses around comparison in operand of &
ping.c:730: warning: unused variable 'k'
ping.c: In function 'ECM1PE':
ping.c:1290: warning: suggest parentheses around comparison in operand of &
ping.c:1443: warning: suggest parentheses around comparison in operand of &
ping.c:1078: warning: unused variable 'k'
ping.c: In function 'ECM2':
ping.c:1506: warning: unused variable 'ee'
ping.c:1506: warning: unused variable 'ggR'
ping.c:1506: warning: unused variable 'ggF'
ping.c:1506: warning: unused variable 'aaR'
ping.c:1506: warning: unused variable 'aaF'
ping.c:1506: warning: unused variable 'etaDiff'
ping.c:1497: warning: unused variable 'k'
ping.c: In function 'ECM2PE':
ping.c:1713: warning: unused variable 'ee'
ping.c:1713: warning: unused variable 'ggR'
ping.c:1713: warning: unused variable 'ggF'
ping.c:1713: warning: unused variable 'aaR'
ping.c:1713: warning: unused variable 'aaF'
ping.c:1713: warning: unused variable 'etaDiff'
ping.c:1704: warning: unused variable 'k'
ping.c: In function 'getInfMat':
ping.c:2557: warning: unused variable 'PhiRw'
ping.c:2557: warning: unused variable 'PhiFw'
ping.c: In function 'getInfMatPE':
ping.c:3007: warning: unused variable 'PhiFRw'
ping.c: In function 'mergePeak':
ping.c:3268: warning: unused variable 'j'
ping.c:3268: warning: unused variable 'i'
ping.c: In function 'BICPE':
ping.c:2133: warning: 'penalty' may be used uninitialized in this function
ping.c: In function 'BIC':
ping.c:2026: warning: 'penalty' may be used uninitialized in this function
ping.c: In function 'fitModelK':
ping.c:457: warning: 'firstFit' may be used uninitialized in this function
ping.c:457: warning: 'ans' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106: warning: suggest parentheses around comparison in operand of &
segment.c:97: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:249: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1294: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1469: warning: suggest parentheses around comparison in operand of &
segment.c:1470: warning: suggest parentheses around comparison in operand of &
segment.c:1471: warning: suggest parentheses around comparison in operand of &
segment.c:1472: warning: suggest parentheses around comparison in operand of &
segment.c:1473: warning: suggest parentheses around comparison in operand of &
segment.c:1419: warning: unused variable 'filter1'
segment.c:1418: warning: unused variable 'muFilter'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PING.so background.o init.o ping.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/PING.Rcheck/PING/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'show' when loading 'GenomeGraphs'
Creating a new generic function for 'map' in package 'PING'
Creating a generic function for 'plot' from package 'graphics' in package 'PING'
** help
*** installing help indices
** building package indices
** installing vignettes
'PING.Rnw'
** testing if installed package can be loaded
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'show' when loading 'GenomeGraphs'
* DONE (PING)