AllelicImbalance 1.7.19
Jesper R Gadin
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AllelicImbalance | | Last Changed Rev: 106363 / Revision: 107602 | | Last Changed Date: 2015-07-14 09:16:34 -0700 (Tue, 14 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 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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### rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.7.19.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.7.19.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AllelicImbalance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AllelicImbalance' version '1.7.19'
* 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 whether package 'AllelicImbalance' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
phase,riskVariant : .local: no visible global function definition for
'phaseArray2Matrix'
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [282s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getSnpIdFromLocation 32.34 0.39 53.58
scanForHeterozygotes-old 12.91 0.01 12.91
import-bam 10.14 0.03 10.33
getAlleleCounts 8.18 0.00 8.42
getAlleleQuality 7.44 0.01 7.46
annotation-wrappers 3.34 0.22 152.57
** running examples for arch 'x64' ... [114s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getSnpIdFromLocation 28.17 0.36 28.54
scanForHeterozygotes-old 14.59 0.00 14.59
import-bam 13.18 0.03 13.21
getAlleleQuality 8.98 0.01 9.00
getAlleleCounts 8.15 0.00 8.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R' [17s]
[17s] OK
** running tests for arch 'x64' ...
Running 'test-all.R' [17s]
[18s] 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: 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.7.19.zip
* DONE (AllelicImbalance)