SomaticSignatures 2.2.3
Julian Gehring
| 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/SomaticSignatures | | Last Changed Rev: 96320 / Revision: 102249 | | Last Changed Date: 2014-11-01 06:38:39 -0700 (Sat, 01 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.2.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SomaticSignatures.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 ‘SomaticSignatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticSignatures’ version ‘2.2.3’
* 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 ‘SomaticSignatures’ can be installed ... [41s/42s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘proxy::as.matrix’ when loading ‘SomaticSignatures’
See ‘/home/biocbuild/bbs-3.0-bioc/meat/SomaticSignatures.Rcheck/00install.out’ for details.
* 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 ... NOTE
scaSNVRanges: no visible global function definition for
‘scaLoadDatasets’
scaSNVRanges: no visible global function definition for ‘scaMetadata’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/23s] 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
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/SomaticSignatures.Rcheck/00check.log’
for details.
* installing *source* package ‘SomaticSignatures’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import by ‘proxy::as.matrix’ when loading ‘SomaticSignatures’
Note: the specification for S3 class “cluster” in package ‘NMF’ seems equivalent to one from package ‘BiocParallel’: 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
Warning: replacing previous import by ‘proxy::as.matrix’ when loading ‘SomaticSignatures’
Note: the specification for S3 class “cluster” in package ‘NMF’ seems equivalent to one from package ‘BiocParallel’: not turning on duplicate class definitions for this class.
* DONE (SomaticSignatures)