PICS 2.10.0
Renan Sauteraud
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PICS | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PICS_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/PICS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PICS’ version ‘2.10.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PICS’ can be installed ... [17s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 dependencies in R code ... NOTE
':::' calls which should be '::':
‘parallel:::detectCores’ ‘parallel:::makeCluster’
‘parallel:::parLapply’ ‘parallel:::stopCluster’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bam2gr: no visible global function definition for ‘elementMetadata’
bam2gr: no visible global function definition for ‘elementMetadata<-’
cand_recursive: no visible global function definition for ‘width’
cand_recursive: no visible global function definition for ‘disjoin’
candidate.region: no visible global function definition for ‘viewMaxs’
candidate.region: no visible global function definition for ‘width’
candidate.region: no visible global function definition for
‘findOverlaps’
makeRangedDataOutput: no visible global function definition for
‘findOverlaps’
s_cut: no visible global function definition for ‘findOverlaps’
s_cut: no visible global function definition for ‘viewMins’
segChrRead: no visible global function definition for ‘findOverlaps’
segChrRead: no visible global function definition for ‘start<-’
segChrRead: no visible global function definition for ‘end<-’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/PICS.Rcheck/00check.log’
for details.
* installing *source* package ‘PICS’ ...
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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pics.c -o pics.o
pics.c: In function ‘iterEM’:
pics.c:581:25: warning: unused variable ‘mu’ [-Wunused-variable]
pics.c: In function ‘ECM1’:
pics.c:803:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
pics.c:963:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
pics.c:651:15: warning: unused variable ‘k’ [-Wunused-variable]
pics.c: In function ‘ECM2’:
pics.c:1009:66: warning: unused variable ‘ee’ [-Wunused-variable]
pics.c:1009:57: warning: unused variable ‘ggR’ [-Wunused-variable]
pics.c:1009:52: warning: unused variable ‘ggF’ [-Wunused-variable]
pics.c:1009:47: warning: unused variable ‘aaR’ [-Wunused-variable]
pics.c:1009:42: warning: unused variable ‘aaF’ [-Wunused-variable]
pics.c:1009:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
pics.c:1009:9: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
pics.c:1000:15: warning: unused variable ‘k’ [-Wunused-variable]
pics.c: In function ‘BIC’:
pics.c:1272:96: warning: unused variable ‘k’ [-Wunused-variable]
pics.c: In function ‘getInfMat’:
pics.c:1633:76: warning: unused variable ‘PhiRw’ [-Wunused-variable]
pics.c:1633:69: warning: unused variable ‘PhiFw’ [-Wunused-variable]
pics.c: In function ‘mergePeak’:
pics.c:1889:11: warning: unused variable ‘j’ [-Wunused-variable]
pics.c:1889:7: warning: unused variable ‘i’ [-Wunused-variable]
pics.c: In function ‘BIC’:
pics.c:1307:6: warning: ‘penalty’ may be used uninitialized in this function [-Wuninitialized]
pics.c: In function ‘fitModelK’:
pics.c:421:18: warning: ‘firstFit’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c segment.c -o segment.o
segment.c: In function ‘segReads’:
segment.c:123:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:114:45: warning: unused variable ‘count’ [-Wunused-variable]
segment.c: In function ‘callRegions’:
segment.c:308:7: warning: unused variable ‘i’ [-Wunused-variable]
segment.c: In function ‘getSegL’:
segment.c:1364:11: warning: unused variable ‘j’ [-Wunused-variable]
segment.c: In function ‘getDensity’:
segment.c:1543:9: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1544:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1545:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1546:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1547:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1548:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1549:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
segment.c:1494:19: warning: variable ‘chr’ set but not used [-Wunused-but-set-variable]
segment.c:1490:8: warning: unused variable ‘filter1’ [-Wunused-variable]
segment.c:1489:11: warning: unused variable ‘muFilter’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o PICS.so pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/PICS.Rcheck/PICS/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: levels, as.factor, elementMetadata, elementMetadata<-
* DONE (PICS)