PICS 2.12.0
Renan Sauteraud
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/PICS | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PICS_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/PICS.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.12.0’
* 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 ... [21s/23s] 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
plot,pics-segReads : .local: warning in symbols((map[, 1] + map[,
2])/2, rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1],
rep(0.6, nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE,
xlim = c(m, M), ylim = c(0, 1)): partial argument match of
'rectangle' to 'rectangles'
plot,pics-segReads : .local: warning in symbols(x@estimates$mu,
rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol = 2, byrow =
TRUE), inches = FALSE, bg = grey(0.5 * pmin(se(x)/50, 1)), fg = 0,
add = TRUE, xlim = c(m, M), ylim = c(0, 1)): partial argument match
of 'rec' to 'rectangles'
plot,pics-segReads : .local: warning in symbols(x@estimates$mu,
rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol = 2, byrow =
TRUE), inches = FALSE, fg = 0, bg = 1, add = TRUE, xlim = c(m, M),
ylim = c(0, 1)): partial argument match of 'rec' to 'rectangles'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] 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
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.1-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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c pics.c -o pics.o
pics.c: In function ‘iterEM’:
pics.c:581: warning: unused variable ‘mu’
pics.c: In function ‘ECM1’:
pics.c:803: warning: suggest parentheses around comparison in operand of &
pics.c:963: warning: suggest parentheses around comparison in operand of &
pics.c:651: warning: unused variable ‘k’
pics.c: In function ‘ECM2’:
pics.c:1009: warning: unused variable ‘ee’
pics.c:1009: warning: unused variable ‘ggR’
pics.c:1009: warning: unused variable ‘ggF’
pics.c:1009: warning: unused variable ‘aaR’
pics.c:1009: warning: unused variable ‘aaF’
pics.c:1009: warning: unused variable ‘etaDiff’
pics.c:1000: warning: unused variable ‘k’
pics.c: In function ‘BIC’:
pics.c:1272: warning: unused variable ‘k’
pics.c: In function ‘getInfMat’:
pics.c:1633: warning: unused variable ‘PhiRw’
pics.c:1633: warning: unused variable ‘PhiFw’
pics.c: In function ‘mergePeak’:
pics.c:1889: warning: unused variable ‘j’
pics.c:1889: warning: unused variable ‘i’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c segment.c -o segment.o
segment.c: In function ‘segReads’:
segment.c:123: warning: suggest parentheses around comparison in operand of &
segment.c:114: warning: unused variable ‘count’
segment.c: In function ‘callRegions’:
segment.c:308: warning: unused variable ‘i’
segment.c: In function ‘getSegL’:
segment.c:1364: warning: unused variable ‘j’
segment.c: In function ‘getDensity’:
segment.c:1543: warning: suggest parentheses around comparison in operand of &
segment.c:1544: warning: suggest parentheses around comparison in operand of &
segment.c:1545: warning: suggest parentheses around comparison in operand of &
segment.c:1546: warning: suggest parentheses around comparison in operand of &
segment.c:1547: warning: suggest parentheses around comparison in operand of &
segment.c:1548: warning: suggest parentheses around comparison in operand of &
segment.c:1549: warning: suggest parentheses around comparison in operand of &
segment.c:1490: warning: unused variable ‘filter1’
segment.c:1489: warning: unused variable ‘muFilter’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o PICS.so pics.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-3.1-bioc/meat/PICS.Rcheck/PICS/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (PICS)