VariantFiltering 1.0.4
Robert Castelo
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/VariantFiltering | | Last Changed Rev: 91489 / Revision: 95116 | | Last Changed Date: 2014-06-16 14:56:15 -0700 (Mon, 16 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 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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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings VariantFiltering_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/VariantFiltering.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantFiltering/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantFiltering’ version ‘1.0.4’
* 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 ‘VariantFiltering’ can be installed ... [21s/21s] 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
PhastConsDb-class 11.701 0.412 12.131
* 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
* installing *source* package ‘VariantFiltering’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function ‘scoss_wm_score_DNAStringSet’:
methods-WeightMatrix.c:122:23: warning: unused variable ‘k’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/VariantFiltering.Rcheck/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (VariantFiltering)