Robert Castelo
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GenomicScores |
| Branch: RELEASE_3_12 |
| Last Commit: 1a877e1 |
| Last Changed Date: 2020-10-27 11:23:24 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:28 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GenomicScores package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 721/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicScores 2.2.0 (landing page) Robert Castelo
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomicScores |
| Version: 2.2.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicScores.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicScores_2.2.0.tar.gz |
| StartedAt: 2021-05-06 03:07:06 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:13:37 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 391.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicScores.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicScores.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicScores_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicScores.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicScores/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicScores' version '2.2.0'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
inst/gscores-template/inst/extdata/.gitkeep
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicScores' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/GScores-class.Rd:240: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/availableGScores.Rd:60: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/availableGScores.Rd:61: file link 'MafDb.1Kgenomes.phase1.hs37d5' in package 'MafDb.1Kgenomes.phase1.hs37d5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/gscores.Rd:110: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/gscores.Rd:111: file link 'MafDb.1Kgenomes.phase1.hs37d5' in package 'MafDb.1Kgenomes.phase1.hs37d5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/rgscores.Rd:57: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/rgscores.Rd:58: file link 'MafDb.1Kgenomes.phase1.hs37d5' in package 'MafDb.1Kgenomes.phase1.hs37d5' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicScores.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
GScores-class 15.11 1.06 19.69
gscores 13.11 1.32 52.79
availableGScores 4.77 2.14 7.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GScores-class 12.16 0.75 14.67
gscores 10.11 1.03 14.42
availableGScores 4.01 0.93 5.12
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicScores.Rcheck/00check.log'
for details.
GenomicScores.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicScores_2.2.0.tar.gz && rm -rf GenomicScores.buildbin-libdir && mkdir GenomicScores.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicScores.buildbin-libdir GenomicScores_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicScores_2.2.0.zip && rm GenomicScores_2.2.0.tar.gz GenomicScores_2.2.0.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
100 1882k 100 1882k 0 0 28.6M 0 --:--:-- --:--:-- --:--:-- 29.1M
install for i386
* installing *source* package 'GenomicScores' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicScores'
finding HTML links ... done
GScores-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/GScores-class.Rd:240: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
GenomicScores-defunct html
GenomicScores-deprecated html
availableGScores html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/availableGScores.Rd:60: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/availableGScores.Rd:61: file link 'MafDb.1Kgenomes.phase1.hs37d5' in package 'MafDb.1Kgenomes.phase1.hs37d5' does not exist and so has been treated as a topic
gscores html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/gscores.Rd:110: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/gscores.Rd:111: file link 'MafDb.1Kgenomes.phase1.hs37d5' in package 'MafDb.1Kgenomes.phase1.hs37d5' does not exist and so has been treated as a topic
igscores html
makeGScoresPackage html
rgscores html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/rgscores.Rd:57: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYvYN7i/R.INSTALL14886cb21955/GenomicScores/man/rgscores.Rd:58: file link 'MafDb.1Kgenomes.phase1.hs37d5' in package 'MafDb.1Kgenomes.phase1.hs37d5' does not exist and so has been treated as a topic
** 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 'GenomicScores' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicScores' as GenomicScores_2.2.0.zip
* DONE (GenomicScores)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenomicScores' successfully unpacked and MD5 sums checked
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GenomicScores.Rcheck/examples_i386/GenomicScores-Ex.timings
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GenomicScores.Rcheck/examples_x64/GenomicScores-Ex.timings
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