IONiseR 1.2.3
Mike Smith
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/IONiseR | | Last Changed Rev: 120784 / Revision: 122332 | | Last Changed Date: 2016-09-07 02:44:08 -0700 (Wed, 07 Sep 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf IONiseR.buildbin-libdir IONiseR.Rcheck && mkdir IONiseR.buildbin-libdir IONiseR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IONiseR.buildbin-libdir IONiseR_1.2.3.tar.gz >IONiseR.Rcheck\00install.out 2>&1 && cp IONiseR.Rcheck\00install.out IONiseR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=IONiseR.buildbin-libdir --install="check:IONiseR-install.out" --force-multiarch --no-vignettes --timings IONiseR_1.2.3.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/IONiseR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IONiseR/DESCRIPTION' ... OK
* this is package 'IONiseR' version '1.2.3'
* 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 whether package 'IONiseR' 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
.get2D: no visible binding for global variable 'full_2D'
.muxToXY: no visible binding for global variable 'matrixCol'
.muxToXY: no visible binding for global variable 'mux'
.muxToXY: no visible binding for global variable 'oddEven'
.muxToXY: no visible binding for global variable 'matrixRow'
.processFastq: no visible binding for global variable 'readIDs'
channelActivityPlot: no visible binding for global variable 'channel'
channelActivityPlot: no visible binding for global variable
'start_time'
channelActivityPlot: no visible binding for global variable 'duration'
channelActivityPlot: no visible binding for global variable 'zvalue'
channelActivityPlot: no visible binding for global variable 'time_bin'
channelActivityPlot: no visible binding for global variable
'mean_value'
layoutPlot: no visible binding for global variable 'channel'
layoutPlot: no visible binding for global variable 'seq_length'
layoutPlot: no visible binding for global variable 'median_signal'
layoutPlot: no visible global function definition for 'error'
muxHeatmap: no visible global function definition for 'right_join'
muxHeatmap: no visible binding for global variable 'channel'
muxHeatmap: no visible binding for global variable 'matrixRow'
muxHeatmap: no visible binding for global variable 'matrixCol'
muxHeatmap: no visible binding for global variable 'meanZValue'
muxHeatmap: no visible binding for global variable 'circleFun'
muxHeatmap: no visible binding for global variable 'x'
muxHeatmap: no visible binding for global variable 'y'
plot2DYield: no visible global function definition for 'inner_join'
plot2DYield: no visible binding for global variable 'start_time'
plot2DYield: no visible binding for global variable 'pass'
plot2DYield: no visible binding for global variable 'nbases'
plot2DYield: no visible binding for global variable 'time_group'
plot2DYield: no visible binding for global variable 'accumulation'
plotActiveChannels: no visible binding for global variable 'start_time'
plotActiveChannels: no visible binding for global variable 'duration'
plotActiveChannels: no visible binding for global variable 'minute'
plotBaseProductionRate: no visible binding for global variable
'start_time'
plotBaseProductionRate: no visible binding for global variable
'bases_called'
plotBaseProductionRate: no visible binding for global variable
'duration'
plotCurrentByTime: no visible binding for global variable 'start_time'
plotCurrentByTime: no visible binding for global variable
'median_signal'
plotEventRate: no visible binding for global variable 'start_time'
plotEventRate: no visible binding for global variable 'num_events'
plotEventRate: no visible binding for global variable 'duration'
plotKmerFrequencyCorrelation: no visible binding for global variable
'full_2D'
plotKmerFrequencyCorrelation: no visible binding for global variable
'start_time'
plotKmerFrequencyCorrelation: no visible binding for global variable
'AAAAA'
plotKmerFrequencyCorrelation: no visible binding for global variable
'TTTTT'
plotKmerFrequencyCorrelation: no visible binding for global variable
'time_group'
plotKmerFrequencyCorrelation: no visible binding for global variable
'freq'
plotKmerFrequencyCorrelation: no visible binding for global variable
'pentamer'
plotKmerFrequencyCorrelation: no visible binding for global variable
'x'
plotKmerFrequencyCorrelation: no visible binding for global variable
'y'
plotReadAccumulation: no visible binding for global variable
'start_time'
plotReadAccumulation: no visible binding for global variable 'minute'
plotReadAccumulation: no visible binding for global variable
'new_reads'
plotReadAccumulation: no visible binding for global variable
'accumulation'
plotReadCategoryCounts: no visible binding for global variable
'full_2D'
plotReadCategoryCounts: no visible binding for global variable 'pass'
plotReadCategoryCounts: no visible binding for global variable
'category'
plotReadTypeProduction: no visible binding for global variable
'start_time'
plotReadTypeProduction: no visible binding for global variable
'time_group'
plotReadTypeProduction: no visible binding for global variable
'full_2D'
plotReadTypeProduction: no visible binding for global variable 'pass'
readFast5Summary: no visible binding for global variable 'start_time'
readFast5Summary: no visible binding for global variable 'duration'
readFast5Summary: no visible binding for global variable 'num_events'
[,Fast5Summary-ANY-ANY: no visible binding for global variable
'baseCalledTemplate'
[,Fast5Summary-ANY-ANY: no visible binding for global variable
'baseCalledComplement'
[,Fast5Summary-ANY-ANY: no visible binding for global variable
'component'
[,Fast5Summary-ANY-ANY: no visible binding for global variable 'idx'
show,Fast5Summary: no visible binding for global variable 'full_2D'
show,Fast5Summary: no visible binding for global variable 'pass'
Undefined global functions or variables:
AAAAA TTTTT accumulation baseCalledComplement baseCalledTemplate
bases_called category channel circleFun component duration error freq
full_2D idx inner_join matrixCol matrixRow meanZValue mean_value
median_signal minute mux nbases new_reads num_events oddEven pass
pentamer readIDs right_join seq_length start_time time_bin time_group
x y zvalue
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'Fast5Summary,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotKmerFrequencyCorrelation 5.14 0.2 5.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotKmerFrequencyCorrelation 5.93 0.24 7.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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 WARNING, 1 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/IONiseR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'IONiseR' ...
** R
** inst
** preparing package for lazy loading
in method for 'readInfo' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
in method for 'rawData' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
in method for 'baseCalled' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
in method for 'fastq' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
in method for '[' with signature '"Fast5Summary","ANY"': no definition for class "Fast5Summary"
in method for 'fastqTemplate' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
in method for 'fastqComplement' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
in method for 'fastq2D' with signature 'x="Fast5Summary"': no definition for class "Fast5Summary"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'IONiseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IONiseR' as IONiseR_1.2.3.zip
* DONE (IONiseR)