BioC 3.4: CHECK report for MethylSeekR on tokay1
This page was generated on 2017-04-15 16:17:40 -0400 (Sat, 15 Apr 2017).
MethylSeekR 1.14.0
Lukas Burger
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MethylSeekR | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: MethylSeekR
|
| Version: 1.14.0
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| Command: rm -rf MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && mkdir MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.14.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.14.0.tar.gz
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| StartedAt: 2017-04-14 23:30:00 -0400 (Fri, 14 Apr 2017)
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| EndedAt: 2017-04-14 23:41:09 -0400 (Fri, 14 Apr 2017)
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| EllapsedTime: 668.4 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:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.14.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MethylSeekR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.14.0'
* 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 'predict'
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: no visible global function definition for 'queryHits'
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'
removeSNPs: no visible global function definition for 'queryHits'
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 'queryHits'
segmentUMRsLMRs: no visible global function definition for
'subjectHits'
segmentUMRsLMRs: no visible global function definition for 'Rle'
segmentUMRsLMRs: no visible global function definition for 'DataFrame'
segmentUMRsLMRs: no visible global function definition for
'colorRampPalette'
Undefined global functions or variables:
DataFrame Rle colorRampPalette nrun predict queryHits runValue
subjectHits
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "predict")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 53.33 4.37 75.39
segmentPMDs 33.64 1.68 35.31
plotPMDSegmentation 31.22 1.63 32.84
savePMDSegments 29.89 1.58 31.47
calculateFDRs 7.06 0.61 25.72
plotAlphaDistributionOneChr 6.69 0.14 6.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 68.04 3.72 89.49
plotPMDSegmentation 38.41 1.44 39.84
savePMDSegments 32.55 1.32 33.86
segmentPMDs 32.00 0.84 32.85
plotAlphaDistributionOneChr 8.78 0.18 8.96
calculateFDRs 7.80 0.64 26.40
* 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:/Users/biocbuild/bbs-3.4-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_1.14.0.zip
* DONE (MethylSeekR)
MethylSeekR.Rcheck/examples_i386/MethylSeekR-Ex.timings:
| name | user | system | elapsed
|
| MethylSeekR-package | 53.33 | 4.37 | 75.39 |
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| calculateFDRs | 7.06 | 0.61 | 25.72 |
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| plotAlphaDistributionOneChr | 6.69 | 0.14 | 6.83 |
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| plotFinalSegmentation | 3.17 | 0.30 | 3.47 |
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| plotPMDSegmentation | 31.22 | 1.63 | 32.84 |
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| readMethylome | 0.56 | 0.03 | 0.59 |
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| readSNPTable | 0.08 | 0.00 | 0.08 |
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| removeSNPs | 0.95 | 0.06 | 1.02 |
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| savePMDSegments | 29.89 | 1.58 | 31.47 |
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| saveUMRLMRSegments | 2.33 | 0.15 | 2.48 |
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| segmentPMDs | 33.64 | 1.68 | 35.31 |
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| segmentUMRsLMRs | 2.57 | 0.15 | 2.72 |
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MethylSeekR.Rcheck/examples_x64/MethylSeekR-Ex.timings:
| name | user | system | elapsed
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| MethylSeekR-package | 68.04 | 3.72 | 89.49 |
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| calculateFDRs | 7.80 | 0.64 | 26.40 |
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| plotAlphaDistributionOneChr | 8.78 | 0.18 | 8.96 |
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| plotFinalSegmentation | 3.39 | 0.34 | 3.73 |
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| plotPMDSegmentation | 38.41 | 1.44 | 39.84 |
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| readMethylome | 0.53 | 0.00 | 0.53 |
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| readSNPTable | 0.11 | 0.00 | 0.11 |
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| removeSNPs | 0.80 | 0.01 | 0.82 |
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| savePMDSegments | 32.55 | 1.32 | 33.86 |
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| saveUMRLMRSegments | 1.94 | 0.01 | 1.95 |
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| segmentPMDs | 32.00 | 0.84 | 32.85 |
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| segmentUMRsLMRs | 1.44 | 0.07 | 1.50 |
|