| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:56 -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 | ||||
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To the developers/maintainers of the motifbreakR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifbreakR.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 1200/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifbreakR 2.8.0 (landing page) Simon Gert Coetzee
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: motifbreakR |
| Version: 2.8.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings motifbreakR_2.8.0.tar.gz |
| StartedAt: 2022-04-12 23:11:32 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:22:27 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 655.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: motifbreakR.Rcheck |
| Warnings: 3 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings motifbreakR_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/motifbreakR.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 'motifbreakR/DESCRIPTION' ... OK
* this is package 'motifbreakR' version '2.8.0'
* 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 'motifbreakR' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/motifbreakR.Rcheck/00install.out' for details.
* 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
* 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
Namespaces in Imports field not imported from:
'compiler' 'grImport'
All declared Imports should be used.
Package in Depends field not imported from: 'MotifDb'
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
formatVcfOut: no visible binding for global variable 'search.genome'
plotMotifLogoStack.2: no visible global function definition for 'par'
preparePWM: no visible binding for global variable 'threshold'
snps.from.file: no visible binding for global variable 'DNA_ALPHABET'
wScore: no visible global function definition for 'scoreMotif'
Undefined global functions or variables:
DNA_ALPHABET par scoreMotif search.genome threshold
Consider adding
importFrom("graphics", "par")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'rs1006140' 'variants.from.file'
Undocumented data sets:
'rs1006140'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'motifbreakR'
'legacy.score'
Undocumented arguments in documentation object 'scoreAllWindows'
'snp.seq' 'snp.seq.rc' 'pwm' 'from' 'to' 'pwm.range' 'calcp'
Undocumented arguments in documentation object 'snps.from.file'
'indels'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
snps.from.rsid 72.71 1.39 85.69
motifbreakR 12.38 1.20 13.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
snps.from.rsid 44.74 1.69 46.50
motifbreakR 16.33 0.34 16.69
* 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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/motifbreakR.Rcheck/00check.log'
for details.
motifbreakR.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/motifbreakR_2.8.0.tar.gz && rm -rf motifbreakR.buildbin-libdir && mkdir motifbreakR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifbreakR.buildbin-libdir motifbreakR_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL motifbreakR_2.8.0.zip && rm motifbreakR_2.8.0.tar.gz motifbreakR_2.8.0.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
64 1790k 64 1156k 0 0 1473k 0 0:00:01 --:--:-- 0:00:01 1472k
100 1790k 100 1790k 0 0 1708k 0 0:00:01 0:00:01 --:--:-- 1709k
install for i386
* installing *source* package 'motifbreakR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
** help
*** installing help indices
converting help for package 'motifbreakR'
finding HTML links ... done
calculatePvalue html
finding level-2 HTML links ... done
encodemotif html
example.results html
factorbook html
hocomoco html
homer html
motifbreakR html
motifbreakR_motif html
plotMB html
scoreAllWindows html
snps.from.file html
snps.from.rsid html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'motifbreakR' ...
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
* MD5 sums
packaged installation of 'motifbreakR' as motifbreakR_2.8.0.zip
* DONE (motifbreakR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'motifbreakR' successfully unpacked and MD5 sums checked
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motifbreakR.Rcheck/examples_i386/motifbreakR-Ex.timings
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motifbreakR.Rcheck/examples_x64/motifbreakR-Ex.timings
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