Marcel Ramos
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/RTCGAToolbox |
| Branch: RELEASE_3_7 |
| Last Commit: 20bfa53 |
| Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:38 -0400 (Wed, 17 Oct 2018).
| Package 1290/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTCGAToolbox 2.10.0 Marcel Ramos
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RTCGAToolbox |
| Version: 2.10.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.10.0.tar.gz |
| StartedAt: 2018-10-17 04:35:44 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:40:27 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 283.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RTCGAToolbox.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RTCGAToolbox.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.10.0'
* 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 'RTCGAToolbox' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Viqx/R.INSTALL23e4d3a2bb8/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-3.7-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 ... NOTE
Namespaces in Imports field not imported from:
'Biobase' 'httr' 'plyr'
All declared Imports should be used.
Unexported object imported by a ':::' call: 'GenomicRanges:::.normarg_field'
See the note in ?`:::` about the use of this operator.
* 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 9.10 0.38 9.62
getGISTICPeaks 1.12 0.35 26.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getReport 7.85 0.17 8.14
getGISTICPeaks 0.82 0.28 31.19
* 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-3.7-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/3.7/bioc/src/contrib/RTCGAToolbox_2.10.0.tar.gz && rm -rf RTCGAToolbox.buildbin-libdir && mkdir RTCGAToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGAToolbox.buildbin-libdir RTCGAToolbox_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RTCGAToolbox_2.10.0.zip && rm RTCGAToolbox_2.10.0.tar.gz RTCGAToolbox_2.10.0.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
41 2539k 41 1056k 0 0 14.5M 0 --:--:-- --:--:-- --:--:-- 15.8M
100 2539k 100 2539k 0 0 28.2M 0 --:--:-- --:--:-- --:--:-- 30.2M
install for i386
* 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-3.7-bioc/tmpdir/Rtmp44Viqx/R.INSTALL23e4d3a2bb8/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
In R CMD INSTALL
install for x64
* installing *source* package 'RTCGAToolbox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGAToolbox' as RTCGAToolbox_2.10.0.zip
* DONE (RTCGAToolbox)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RTCGAToolbox' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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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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