Simon Gert Coetzee
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/motifbreakR |
| Branch: RELEASE_3_8 |
| Last Commit: c35ebfb |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:53 -0400 (Sat, 13 Apr 2019).
| Package 993/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifbreakR 1.12.0 Simon Gert Coetzee
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: motifbreakR |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifbreakR_1.12.0.tar.gz |
| StartedAt: 2019-04-13 03:57:46 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:08:15 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 629.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: motifbreakR.Rcheck |
| Warnings: 1 |
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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:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifbreakR_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifbreakR.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 'motifbreakR/DESCRIPTION' ... OK
* this is package 'motifbreakR' version '1.12.0'
* 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 'motifbreakR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
See 'C:/Users/biocbuild/bbs-3.8-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
Packages in Depends field not imported from:
'MotifDb' 'grid'
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
plotMotifLogoStack.2: no visible global function definition for 'par'
snps.from.file: no visible global function definition for 'info'
snps.from.file: no visible global function definition for 'rowRanges'
snps.from.rsid: no visible global function definition for 'snpsById'
Undefined global functions or variables:
info par rowRanges snpsById
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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
snps.from.rsid 47.58 1.40 59.74
motifbreakR 5.71 0.34 6.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
snps.from.rsid 52.91 1.72 54.65
motifbreakR 5.50 0.15 5.66
* 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifbreakR.Rcheck/00check.log'
for details.
motifbreakR.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/motifbreakR_1.12.0.tar.gz && rm -rf motifbreakR.buildbin-libdir && mkdir motifbreakR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifbreakR.buildbin-libdir motifbreakR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL motifbreakR_1.12.0.zip && rm motifbreakR_1.12.0.tar.gz motifbreakR_1.12.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1356k 100 1356k 0 0 26.4M 0 --:--:-- --:--:-- --:--:-- 28.7M
install for i386
* installing *source* package 'motifbreakR' ...
** 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'
** 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
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
factorbook html
hocomoco html
homer html
motifbreakR html
motifbreakR_motif html
plotMB html
snps.from.file html
snps.from.rsid html
** building package indices
** installing vignettes
** 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'
In R CMD INSTALL
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'
* MD5 sums
packaged installation of 'motifbreakR' as motifbreakR_1.12.0.zip
* DONE (motifbreakR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'motifbreakR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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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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