Lukas Burger
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MethylSeekR |
| Branch: RELEASE_3_8 |
| Last Commit: b1eb0e5 |
| Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:37 -0400 (Sat, 13 Apr 2019).
| Package 943/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MethylSeekR 1.22.0 Lukas Burger
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MethylSeekR |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylSeekR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MethylSeekR_1.22.0.tar.gz |
| StartedAt: 2019-04-13 03:45:41 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:57:34 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 713.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethylSeekR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylSeekR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MethylSeekR_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MethylSeekR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 63.45 4.00 80.46
plotPMDSegmentation 45.13 1.31 46.45
savePMDSegments 44.50 1.08 45.58
segmentPMDs 41.99 0.61 42.61
plotAlphaDistributionOneChr 13.40 0.41 13.83
calculateFDRs 8.19 0.65 20.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 53.31 2.12 67.21
plotPMDSegmentation 27.79 0.84 28.64
segmentPMDs 27.00 0.61 27.61
savePMDSegments 24.76 0.55 25.31
calculateFDRs 6.22 0.06 18.22
plotAlphaDistributionOneChr 5.80 0.08 5.87
* 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-3.8-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.
MethylSeekR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MethylSeekR_1.22.0.tar.gz && rm -rf MethylSeekR.buildbin-libdir && mkdir MethylSeekR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylSeekR.buildbin-libdir MethylSeekR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MethylSeekR_1.22.0.zip && rm MethylSeekR_1.22.0.tar.gz MethylSeekR_1.22.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1074k 100 1074k 0 0 16.9M 0 --:--:-- --:--:-- --:--:-- 17.7M
install for i386
* installing *source* package 'MethylSeekR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MethylSeekR'
finding HTML links ... done
MethylSeekR-package html
calculateFDRs html
plotAlphaDistributionOneChr html
plotFinalSegmentation html
plotPMDSegmentation html
readMethylome html
readSNPTable html
removeSNPs html
savePMDSegments html
saveUMRLMRSegments html
segmentPMDs html
segmentUMRsLMRs html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MethylSeekR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylSeekR' as MethylSeekR_1.22.0.zip
* DONE (MethylSeekR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MethylSeekR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
MethylSeekR.Rcheck/examples_i386/MethylSeekR-Ex.timings
|
MethylSeekR.Rcheck/examples_x64/MethylSeekR-Ex.timings
|