vtpnet 0.4.1
VJ Carey
| 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/vtpnet | | Last Changed Rev: 92710 / Revision: 95116 | | Last Changed Date: 2014-07-22 11:21:10 -0700 (Tue, 22 Jul 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | 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 --no-multiarch vtpnet_0.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/vtpnet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vtpnet/DESCRIPTION’ ... OK
* this is package ‘vtpnet’ version ‘0.4.1’
* 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 ‘vtpnet’ can be installed ... [8s/8s] OK
* checking installed package size ... NOTE
installed size is 30.7Mb
sub-directories of 1Mb or more:
data 30.5Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
‘doParallel’ ‘foreach’
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
‘GenomicRanges’ ‘graph’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rng2facHits: warning in dir(patt = "rda$"): partial argument match of
'patt' to 'pattern'
runfimo: warning in dir(patt = "_out"): partial argument match of
'patt' to 'pattern'
gwMatchPWM: no visible binding for global variable ‘Hsapiens’
gwMatchPWM: no visible global function definition for ‘%dopar%’
gwMatchPWM: no visible global function definition for ‘foreach’
gwMatchPWM: no visible binding for global variable ‘i’
rng2facHits: no visible global function definition for
‘registerDoParallel’
rng2facHits: no visible global function definition for ‘%dopar%’
rng2facHits: no visible global function definition for ‘foreach’
rng2facHits: no visible binding for global variable ‘i’
runfimo: no visible global function definition for ‘%dopar%’
runfimo: no visible global function definition for ‘foreach’
runfimo: no visible binding for global variable ‘i’
setupGWPM: no visible global function definition for
‘registerDoParallel’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘MdbSearchToDisk’ ‘filterGWASbyMap’ ‘getMtags’ ‘getOneHits’
‘gwMatchPWM’ ‘matrc’ ‘rng2facHits’ ‘runfimo’ ‘setupGWPM’
Undocumented data sets:
‘cancerMap’ ‘maurGWAS’ ‘pax4’ ‘pax4_75’ ‘pax4_85’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
no parsed files found
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
maurGWAS.rda 103Kb 76Kb xz
pax4.rda 25.9Mb 17.5Mb xz
pax4_75.rda 4.5Mb 2.3Mb xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘ShortRead’
* 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
WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/vtpnet.Rcheck/00check.log’
for details.