Marcel Ramos
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RTCGAToolbox |
| Branch: master |
| Last Commit: 90e3be0 |
| Last Changed Date: 2019-04-04 20:18:02 -0400 (Thu, 04 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:24:07 -0400 (Tue, 09 Apr 2019).
| Package 1403/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTCGAToolbox 2.13.9 Marcel Ramos
| 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: RTCGAToolbox |
| Version: 2.13.9 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.13.9.tar.gz |
| StartedAt: 2019-04-09 05:40:45 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:45:13 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 268.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RTCGAToolbox.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:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.13.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTCGAToolbox.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 'RTCGAToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCGAToolbox' version '2.13.9'
* 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 'RTCGAToolbox' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpQjMwcq/R.INSTALLd20618a58fb/RTCGAToolbox/man/biocExtract.Rd:32: file link 'RaggedExperiment' in package 'RaggedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTCGAToolbox.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 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
getReport 6.06 0.58 6.64
getGISTICPeaks 0.93 0.11 7.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getReport 7.61 0.24 7.89
getGISTICPeaks 0.64 0.14 5.99
* 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
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTCGAToolbox.Rcheck/00check.log'
for details.
RTCGAToolbox.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/RTCGAToolbox_2.13.9.tar.gz && rm -rf RTCGAToolbox.buildbin-libdir && mkdir RTCGAToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGAToolbox.buildbin-libdir RTCGAToolbox_2.13.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RTCGAToolbox_2.13.9.zip && rm RTCGAToolbox_2.13.9.tar.gz RTCGAToolbox_2.13.9.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
20 2538k 20 528k 0 0 3416k 0 --:--:-- --:--:-- --:--:-- 3567k
100 2538k 100 2538k 0 0 7539k 0 --:--:-- --:--:-- --:--:-- 7692k
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'RTCGAToolbox/inst/NEWS' to 'RTCGAToolbox/NEWS.md'
* installing *source* package 'RTCGAToolbox' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RTCGAToolbox'
finding HTML links ... done
CorResult-class html
DGEResult-class html
FirehoseCGHArray-class html
FirehoseData-class html
FirehoseGISTIC-class html
FirehoseMethylationArray-class html
FirehosemRNAArray-class html
RTCGASample html
RTCGAToolbox html
biocExtract html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpQjMwcq/R.INSTALLd20618a58fb/RTCGAToolbox/man/biocExtract.Rd:32: file link 'RaggedExperiment' in package 'RaggedExperiment' does not exist and so has been treated as a topic
getBroadSubtypes html
getCNGECorrelation html
getData html
getDiffExpressedGenes html
getFirehoseAnalyzeDates html
getFirehoseData html
getFirehoseDatasets html
getFirehoseRunningDates html
getGISTICPeaks html
getMutationRate html
getReport html
getSurvival html
hg19.ucsc.gene.locations html
selectType html
showResults-CorResult html
showResults-DGEResult html
showResults 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
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'RTCGAToolbox/inst/NEWS' to 'RTCGAToolbox/NEWS.md'
* installing *source* package 'RTCGAToolbox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGAToolbox' as RTCGAToolbox_2.13.9.zip
* DONE (RTCGAToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RTCGAToolbox' successfully unpacked and MD5 sums checked
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RTCGAToolbox.Rcheck/examples_i386/RTCGAToolbox-Ex.timings
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RTCGAToolbox.Rcheck/examples_x64/RTCGAToolbox-Ex.timings
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