AllelicImbalance 1.8.0
Jesper R Gadin
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AllelicImbalance | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘AllelicImbalance’ can be installed ... [24s/24s] 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 loading without being on the library search path ... 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
countAllelesFromBam,GRanges : .local: no visible binding for global
variable ‘UserDir’
detectAI,ASEset : .local: no visible binding for global variable
‘tf.keep1’
detectAI,ASEset : .local: no visible binding for global variable
‘tf.keep2’
detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI : .local:
no visible binding for global variable ‘grid.arrange’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local :
<anonymous>: no visible global function definition for
‘panel.smoothScatter’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local :
<anonymous>: no visible global function definition for
‘panel.linejoin’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local: no visible
global function definition for ‘doubleYScale’
frequency_vs_threshold_variable_multigraph_plot,DetectedAI : .local: no
visible binding for global variable ‘grid.arrange’
frequency_vs_threshold_variable_plot,DetectedAI : .local : <anonymous>:
no visible global function definition for ‘panel.smoothScatter’
frequency_vs_threshold_variable_plot,DetectedAI : .local : <anonymous>:
no visible global function definition for ‘panel.linejoin’
frequency_vs_threshold_variable_plot,DetectedAI : .local: no visible
global function definition for ‘doubleYScale’
getSnpIdFromLocation,GRanges : .local: no visible global function
definition for ‘getSNPlocs’
reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI
: .local: no visible binding for global variable ‘grid.arrange’
reference_frequency_density_vs_threshold_variable_plot,DetectedAI :
.local: no visible global function definition for ‘levelplot’
* 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 ... NOTE
Error in nrow(x@elementMetadata) :
error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "ASEset"
Calls: <Anonymous> ... withCallingHandlers -> check_one -> length -> length -> nrow
Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [87s/87s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getSnpIdFromLocation 21.277 0.188 21.498
import-bam 10.615 0.020 10.659
scanForHeterozygotes-old 9.928 0.088 10.019
annotation-wrappers 6.519 0.072 6.593
getAlleleQuality 6.437 0.000 6.437
getAlleleCounts 5.971 0.000 5.979
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [11s/11s]
[11s/11s] 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
‘/home/biocbuild/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.
* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘binom.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘chisq.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘AllelicImbalance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)