BioC 3.4: CHECK report for MEDIPS on tokay1
This page was generated on 2017-04-15 16:16:24 -0400 (Sat, 15 Apr 2017).
MEDIPS 1.24.0
Lukas Chavez
| 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/MEDIPS | | 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 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: MEDIPS
|
| Version: 1.24.0
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| Command: rm -rf MEDIPS.buildbin-libdir MEDIPS.Rcheck && mkdir MEDIPS.buildbin-libdir MEDIPS.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEDIPS.buildbin-libdir MEDIPS_1.24.0.tar.gz >MEDIPS.Rcheck\00install.out 2>&1 && cp MEDIPS.Rcheck\00install.out MEDIPS-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MEDIPS.buildbin-libdir --install="check:MEDIPS-install.out" --force-multiarch --no-vignettes --timings MEDIPS_1.24.0.tar.gz
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| StartedAt: 2017-04-14 23:22:15 -0400 (Fri, 14 Apr 2017)
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| EndedAt: 2017-04-14 23:30:19 -0400 (Fri, 14 Apr 2017)
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| EllapsedTime: 483.9 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: MEDIPS.Rcheck
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| Warnings: 0
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Command output
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### Running command:
###
### rm -rf MEDIPS.buildbin-libdir MEDIPS.Rcheck && mkdir MEDIPS.buildbin-libdir MEDIPS.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEDIPS.buildbin-libdir MEDIPS_1.24.0.tar.gz >MEDIPS.Rcheck\00install.out 2>&1 && cp MEDIPS.Rcheck\00install.out MEDIPS-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MEDIPS.buildbin-libdir --install="check:MEDIPS-install.out" --force-multiarch --no-vignettes --timings MEDIPS_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MEDIPS.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 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.24.0'
* 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 'MEDIPS' 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
MEDIPS.CpGenrich: no visible global function definition for 'seqlevels'
MEDIPS.CpGenrich: no visible global function definition for
'seqlengths'
MEDIPS.CpGenrich: no visible global function definition for 'new'
MEDIPS.addCNV: no visible global function definition for 'seqnames'
MEDIPS.correlation: no visible global function definition for 'pdf'
MEDIPS.correlation: no visible global function definition for 'dev.off'
MEDIPS.couplingVector: no visible global function definition for 'new'
MEDIPS.createROIset: no visible global function definition for
'seqnames'
MEDIPS.createROIset: no visible global function definition for
'seqlengths'
MEDIPS.createROIset: no visible global function definition for 'new'
MEDIPS.createSet: no visible global function definition for 'seqnames'
MEDIPS.createSet: no visible global function definition for
'seqlengths'
MEDIPS.createSet: no visible global function definition for 'seqlevels'
MEDIPS.createSet: no visible global function definition for 'new'
MEDIPS.diffMeth: no visible global function definition for 'p.adjust'
MEDIPS.exportWIG: no visible global function definition for 'seqnames'
MEDIPS.mergeSets: no visible global function definition for 'new'
MEDIPS.meth: no visible global function definition for 'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
'points'
MEDIPS.plotSeqCoverage: no visible global function definition for 'pie'
MEDIPS.plotSeqCoverage: no visible global function definition for
'hist'
MEDIPS.saturation: no visible global function definition for
'seqlevels'
MEDIPS.saturation: no visible global function definition for
'seqlengths'
MEDIPS.selectROIs: no visible global function definition for
'elementMetadata<-'
MEDIPS.selectROIs: no visible global function definition for
'elementMetadata'
MEDIPS.selectROIs: no visible global function definition for
'findOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'seqnames'
MEDIPS.seqCoverage: no visible global function definition for
'seqlevels'
MEDIPS.seqCoverage: no visible global function definition for
'seqlengths'
MEDIPS.setAnnotation: no visible global function definition for
'findOverlaps'
getGRange: no visible global function definition for 'qpois'
getGRange: no visible global function definition for 'seqlengths'
getGRange: no visible global function definition for 'countMatches'
getGRange: no visible global function definition for 'strand<-'
getMObjectFromWIG: no visible global function definition for
'seqlengths'
getMObjectFromWIG: no visible global function definition for
'runLength'
getMObjectFromWIG: no visible global function definition for 'seqnames'
getMObjectFromWIG: no visible global function definition for 'runValue'
getMObjectFromWIG: no visible global function definition for 'new'
getPairedGRange: no visible global function definition for 'sd'
getPairedGRange: no visible global function definition for 'qpois'
getPairedGRange: no visible global function definition for 'seqlengths'
getPairedGRange: no visible global function definition for
'countMatches'
getPairedGRange: no visible global function definition for 'strand<-'
matSd: no visible binding for global variable 'sd'
matTtest: no visible binding for global variable 'sd'
matTtest: no visible global function definition for 'pt'
Undefined global functions or variables:
countMatches dev.off elementMetadata elementMetadata<- findOverlaps
hist new p.adjust pdf pie points pt qpois runLength runValue sd
seqlengths seqlevels seqnames strand<-
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "hist", "pie", "points")
importFrom("methods", "new")
importFrom("stats", "p.adjust", "pt", "qpois", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
MEDIPS.meth 51.91 2.22 54.20
MEDIPS.addCNV 26.72 0.70 28.40
MEDIPS.saturation 5.48 0.02 5.50
MEDIPS.plotSaturation 5.04 0.23 5.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MEDIPS.meth 41.86 1.92 43.78
MEDIPS.addCNV 25.17 0.57 25.73
MEDIPS.plotSaturation 5.98 0.20 6.18
MEDIPS.saturation 5.17 0.09 5.26
* 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
'C:/Users/biocbuild/bbs-3.4-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.
MEDIPS.Rcheck/00install.out:
install for i386
* installing *source* package 'MEDIPS' ...
** 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 'MEDIPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEDIPS' as MEDIPS_1.24.0.zip
* DONE (MEDIPS)
MEDIPS.Rcheck/examples_i386/MEDIPS-Ex.timings:
| name | user | system | elapsed
|
| COUPLINGset-class | 0 | 0 | 0 |
|
| MEDIPS.CpGenrich | 0.06 | 0.00 | 0.11 |
|
| MEDIPS.addCNV | 26.72 | 0.70 | 28.40 |
|
| MEDIPS.correlation | 1.11 | 0.04 | 1.60 |
|
| MEDIPS.couplingVector | 2.86 | 0.03 | 2.89 |
|
| MEDIPS.createROIset | 0.85 | 0.03 | 1.08 |
|
| MEDIPS.createSet | 0.81 | 0.06 | 0.88 |
|
| MEDIPS.exportWIG | 1.52 | 0.05 | 1.56 |
|
| MEDIPS.getAnnotation | 0 | 0 | 0 |
|
| MEDIPS.mergeFrames | 0.01 | 0.00 | 0.01 |
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| MEDIPS.mergeSets | 0.39 | 0.03 | 0.54 |
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| MEDIPS.meth | 51.91 | 2.22 | 54.20 |
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| MEDIPS.plotCalibrationPlot | 3.96 | 0.20 | 4.16 |
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| MEDIPS.plotSaturation | 5.04 | 0.23 | 5.28 |
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| MEDIPS.plotSeqCoverage | 3.35 | 0.08 | 3.42 |
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| MEDIPS.saturation | 5.48 | 0.02 | 5.50 |
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| MEDIPS.selectROIs | 3.50 | 0.01 | 3.52 |
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| MEDIPS.selectSig | 3.88 | 0.11 | 3.98 |
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| MEDIPS.seqCoverage | 2.97 | 0.14 | 3.11 |
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| MEDIPS.setAnnotation | 3.26 | 0.10 | 3.36 |
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| MEDIPSroiSet-class | 0 | 0 | 0 |
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| MEDIPSset-class | 0 | 0 | 0 |
|
MEDIPS.Rcheck/examples_x64/MEDIPS-Ex.timings:
| name | user | system | elapsed
|
| COUPLINGset-class | 0 | 0 | 0 |
|
| MEDIPS.CpGenrich | 0.05 | 0.00 | 0.05 |
|
| MEDIPS.addCNV | 25.17 | 0.57 | 25.73 |
|
| MEDIPS.correlation | 1.05 | 0.03 | 1.08 |
|
| MEDIPS.couplingVector | 3.09 | 0.04 | 3.14 |
|
| MEDIPS.createROIset | 0.86 | 0.02 | 0.88 |
|
| MEDIPS.createSet | 0.86 | 0.09 | 0.96 |
|
| MEDIPS.exportWIG | 1.72 | 0.00 | 1.73 |
|
| MEDIPS.getAnnotation | 0 | 0 | 0 |
|
| MEDIPS.mergeFrames | 0 | 0 | 0 |
|
| MEDIPS.mergeSets | 0.53 | 0.00 | 0.53 |
|
| MEDIPS.meth | 41.86 | 1.92 | 43.78 |
|
| MEDIPS.plotCalibrationPlot | 3.42 | 0.13 | 3.55 |
|
| MEDIPS.plotSaturation | 5.98 | 0.20 | 6.18 |
|
| MEDIPS.plotSeqCoverage | 3.05 | 0.03 | 3.08 |
|
| MEDIPS.saturation | 5.17 | 0.09 | 5.26 |
|
| MEDIPS.selectROIs | 2.49 | 0.07 | 2.55 |
|
| MEDIPS.selectSig | 3.38 | 0.12 | 3.50 |
|
| MEDIPS.seqCoverage | 2.83 | 0.13 | 2.95 |
|
| MEDIPS.setAnnotation | 2.50 | 0.15 | 2.66 |
|
| MEDIPSroiSet-class | 0 | 0 | 0 |
|
| MEDIPSset-class | 0 | 0 | 0 |
|