BioC 3.3: CHECK report for MethylSeekR on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:11 -0400 (Tue, 27 Oct 2015).
MethylSeekR 1.11.0
Lukas Burger
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MethylSeekR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
Summary
| Package: MethylSeekR
|
| Version: 1.11.0
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| Command: rm -rf MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && mkdir MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.11.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.11.0.tar.gz
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| StartedAt: 2015-10-27 04:05:21 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 04:14:47 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 566.6 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: MethylSeekR.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && mkdir MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.11.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.11.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/MethylSeekR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '1.11.0'
* 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 'MethylSeekR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'parallel'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'geneplotter'
All declared Imports should be used.
Package in Depends field not imported from: 'rtracklayer'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'Rle'
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'runValue'
calculateAlphaDistr : <anonymous>: no visible global function
definition for 'Rle'
calculateFDRs : <anonymous>: no visible global function definition for
'Rle'
calculateFDRs : <anonymous>: no visible global function definition for
'runValue'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'Rle'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'nrun'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'runValue'
plotFinalSegmentation: no visible global function definition for 'Rle'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'Rle'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'runValue'
segmentUMRsLMRs: no visible global function definition for 'Rle'
segmentUMRsLMRs: no visible global function definition for 'DataFrame'
Undefined global functions or variables:
DataFrame Rle nrun runValue
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [201s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 50.15 3.55 67.86
plotPMDSegmentation 31.02 0.97 31.98
savePMDSegments 29.72 1.05 30.76
segmentPMDs 29.68 0.70 30.39
calculateFDRs 7.14 0.75 20.62
plotAlphaDistributionOneChr 6.56 0.29 6.86
** running examples for arch 'x64' ... [218s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 55.47 3.42 72.51
plotPMDSegmentation 35.09 1.20 36.30
savePMDSegments 32.54 1.03 33.56
segmentPMDs 32.17 1.07 33.25
calculateFDRs 7.39 0.62 21.01
plotAlphaDistributionOneChr 7.55 0.38 7.92
* 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: 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.
MethylSeekR.Rcheck/00install.out:
install for i386
* installing *source* package 'MethylSeekR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'MethylSeekR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylSeekR' as MethylSeekR_1.11.0.zip
* DONE (MethylSeekR)
MethylSeekR.Rcheck/examples_i386/MethylSeekR-Ex.timings:
| name | user | system | elapsed
|
| MethylSeekR-package | 50.15 | 3.55 | 67.86 |
|
| calculateFDRs | 7.14 | 0.75 | 20.62 |
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| plotAlphaDistributionOneChr | 6.56 | 0.29 | 6.86 |
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| plotFinalSegmentation | 2.78 | 0.36 | 3.14 |
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| plotPMDSegmentation | 31.02 | 0.97 | 31.98 |
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| readMethylome | 0.50 | 0.02 | 0.52 |
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| readSNPTable | 0.08 | 0.01 | 0.09 |
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| removeSNPs | 0.62 | 0.03 | 0.66 |
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| savePMDSegments | 29.72 | 1.05 | 30.76 |
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| saveUMRLMRSegments | 1.65 | 0.10 | 1.73 |
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| segmentPMDs | 29.68 | 0.70 | 30.39 |
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| segmentUMRsLMRs | 1.77 | 0.06 | 1.83 |
|
MethylSeekR.Rcheck/examples_x64/MethylSeekR-Ex.timings:
| name | user | system | elapsed
|
| MethylSeekR-package | 55.47 | 3.42 | 72.51 |
|
| calculateFDRs | 7.39 | 0.62 | 21.01 |
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| plotAlphaDistributionOneChr | 7.55 | 0.38 | 7.92 |
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| plotFinalSegmentation | 3.30 | 0.25 | 3.55 |
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| plotPMDSegmentation | 35.09 | 1.20 | 36.30 |
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| readMethylome | 0.52 | 0.05 | 0.56 |
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| readSNPTable | 0.08 | 0.00 | 0.07 |
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| removeSNPs | 0.59 | 0.03 | 0.63 |
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| savePMDSegments | 32.54 | 1.03 | 33.56 |
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| saveUMRLMRSegments | 1.65 | 0.10 | 1.75 |
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| segmentPMDs | 32.17 | 1.07 | 33.25 |
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| segmentUMRsLMRs | 1.69 | 0.04 | 1.72 |
|