Lukas Burger
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/MethylSeekR |
| git_branch: RELEASE_3_14 |
| git_last_commit: 6a74421 |
| git_last_commit_date: 2021-10-26 12:06:33 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:53 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the MethylSeekR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylSeekR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1127/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethylSeekR 1.34.0 (landing page) Lukas Burger
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MethylSeekR |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylSeekR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MethylSeekR_1.34.0.tar.gz |
| StartedAt: 2022-04-12 22:43:59 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 22:55:08 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 668.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethylSeekR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylSeekR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MethylSeekR_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MethylSeekR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.34.0'
* 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 'values'
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 'values'
calculateFDRs: no visible global function definition for 'queryHits'
calculateFDRs: no visible global function definition for 'values<-'
calculateFDRs : <anonymous>: no visible global function definition for
'Rle'
calculateFDRs : <anonymous>: no visible global function definition for
'values'
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'
plotAlphaDistributionOneChr: no visible global function definition for
'values'
plotFinalSegmentation: no visible global function definition for
'values'
plotFinalSegmentation: no visible global function definition for 'Rle'
plotPMDSegmentation: no visible global function definition for 'values'
readMethylome: no visible global function definition for 'values'
removeSNPs: no visible global function definition for 'queryHits'
savePMDSegments: no visible global function definition for 'values'
saveUMRLMRSegments: no visible global function definition for 'values'
segmentUMRsLMRs: no visible global function definition for 'values'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'Rle'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'values'
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 'values<-'
segmentUMRsLMRs: no visible global function definition for 'DataFrame'
segmentUMRsLMRs: no visible global function definition for
'colorRampPalette'
trainPMDHMM: no visible global function definition for 'values'
Undefined global functions or variables:
DataFrame Rle colorRampPalette nrun predict queryHits runValue
subjectHits values values<-
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 (user + system) or elapsed time > 5s
user system elapsed
MethylSeekR-package 67.59 5.00 78.50
segmentPMDs 40.55 1.26 41.81
plotPMDSegmentation 40.41 1.39 41.80
savePMDSegments 40.25 1.11 41.36
plotAlphaDistributionOneChr 12.80 0.14 12.93
calculateFDRs 9.53 0.28 15.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MethylSeekR-package 48.56 1.77 58.70
plotPMDSegmentation 30.66 1.11 31.80
savePMDSegments 28.94 0.73 29.67
segmentPMDs 29.13 0.54 29.67
calculateFDRs 11.26 0.39 17.50
plotAlphaDistributionOneChr 6.62 0.25 6.88
* 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-3.14-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.
MethylSeekR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MethylSeekR_1.34.0.tar.gz && rm -rf MethylSeekR.buildbin-libdir && mkdir MethylSeekR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylSeekR.buildbin-libdir MethylSeekR_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MethylSeekR_1.34.0.zip && rm MethylSeekR_1.34.0.tar.gz MethylSeekR_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
78 1073k 78 838k 0 0 1151k 0 --:--:-- --:--:-- --:--:-- 1151k
100 1073k 100 1073k 0 0 1255k 0 --:--:-- --:--:-- --:--:-- 1256k
install for i386
* installing *source* package 'MethylSeekR' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MethylSeekR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylSeekR' as MethylSeekR_1.34.0.zip
* DONE (MethylSeekR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MethylSeekR' successfully unpacked and MD5 sums checked
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MethylSeekR.Rcheck/examples_i386/MethylSeekR-Ex.timings
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MethylSeekR.Rcheck/examples_x64/MethylSeekR-Ex.timings
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