R. Taylor Raborn
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TSRchitect |
| Branch: master |
| Last Commit: e62c8d3 |
| Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:31:06 -0400 (Tue, 09 Apr 2019).
| Package 1648/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TSRchitect 1.9.0 R. Taylor Raborn
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: TSRchitect |
| Version: 1.9.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSRchitect.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TSRchitect_1.9.0.tar.gz |
| StartedAt: 2019-04-09 06:30:57 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:38:13 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 435.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TSRchitect.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSRchitect.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TSRchitect_1.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TSRchitect/DESCRIPTION' ... OK
* this is package 'TSRchitect' version '1.9.0'
* 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 'TSRchitect' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:37: file link 'import.bed' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:38: file link 'import.gff' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:39: file link 'import.gff3' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationHub-methods.Rd:44: file link 'AnnotationHub' in package 'AnnotationHub' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TSRchitect.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 ... NOTE
File
inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
loadTSSobj-methods 8.39 0.64 10.39
processTSS-methods 0.25 0.11 45.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
loadTSSobj-methods 7.23 0.11 7.34
processTSS-methods 0.42 0.09 78.89
* 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-3.9-bioc/meat/TSRchitect.Rcheck/00check.log'
for details.
TSRchitect.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TSRchitect_1.9.0.tar.gz && rm -rf TSRchitect.buildbin-libdir && mkdir TSRchitect.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSRchitect.buildbin-libdir TSRchitect_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TSRchitect_1.9.0.zip && rm TSRchitect_1.9.0.tar.gz TSRchitect_1.9.0.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 2041k 100 2041k 0 0 23.3M 0 --:--:-- --:--:-- --:--:-- 25.2M
install for i386
* installing *source* package 'TSRchitect' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TSRchitect'
finding HTML links ... done
TSRchitectUsersGuide html
addAnnotationToTSR-methods html
finding level-2 HTML links ... done
addTagCountsToTSR-methods html
bedToTSS-methods html
cDNAtoBED-methods html
createSummarizedExperiment-methods html
detTSR-methods html
determineTSR-methods html
getBamData-methods html
getFileNames-methods html
getTSRdata-methods html
getTSScountData-methods html
getTSStagData-methods html
getTitle-methods html
importAnnotationExternal-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:37: file link 'import.bed' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:38: file link 'import.gff' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:39: file link 'import.gff3' in package 'rtracklayer' does not exist and so has been treated as a topic
importAnnotationHub-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationHub-methods.Rd:44: file link 'AnnotationHub' in package 'AnnotationHub' does not exist and so has been treated as a topic
inputToTSS-methods html
loadTSSobj-methods html
makeGRangesFromTSR-methods html
mergeSampleData-methods html
processTSS-methods html
tsrCluster html
tssObject html
writeTSR-methods html
** building package indices
** installing vignettes
'TSRchitect.Rmd' using 'UTF-8'
'TSRchitectUsersGuide.Rmd' using 'UTF-8'
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), :
number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), :
number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), :
number of items to replace is not a multiple of replacement length
** 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 'TSRchitect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSRchitect' as TSRchitect_1.9.0.zip
* DONE (TSRchitect)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TSRchitect' successfully unpacked and MD5 sums checked
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TSRchitect.Rcheck/examples_i386/TSRchitect-Ex.timings
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TSRchitect.Rcheck/examples_x64/TSRchitect-Ex.timings
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