VJ Carey
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BiocOncoTK |
| Branch: RELEASE_3_8 |
| Last Commit: 078e833 |
| Last Changed Date: 2019-01-04 13:03:51 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:17 -0400 (Sat, 13 Apr 2019).
| Package 140/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocOncoTK 1.2.1 VJ Carey
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BiocOncoTK |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocOncoTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocOncoTK_1.2.1.tar.gz |
| StartedAt: 2019-04-13 00:46:46 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:51:05 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 259.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocOncoTK.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocOncoTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocOncoTK_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocOncoTK.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 'BiocOncoTK/DESCRIPTION' ... OK * this is package 'BiocOncoTK' version '1.2.1' * package encoding: UTF-8 * 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 'BiocOncoTK' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: 'DBI' A package should be listed in only one of these fields. * 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 ... NOTE .rainfall.bq.df: no visible global function definition for 'seqlengths' .rainfall.maeGRL.df: no visible global function definition for 'genome' .rainfall.maeGRL.df: no visible global function definition for 'seqlengths' checkCache_patel: no visible global function definition for 'BiocFileCache' chrbounds_basic: no visible global function definition for 'seqlengths' ggFeatDens : <anonymous>: no visible binding for global variable 'Consequence' ggFeatDens: no visible binding for global variable 'tfstart' ggFeatureSegs: no visible global function definition for 'genes' ggFeatureSegs: no visible binding for global variable 'symbol' ggMutDens : <anonymous>: no visible binding for global variable 'Consequence' ggMutDens: no visible binding for global variable 'project_short_name' mc3toGR : <anonymous>: no visible binding for global variable 'Consequence' rainfall: no visible global function definition for 'genome' tumNorSet : <anonymous>: no visible global function definition for 'pancan_SE' Undefined global functions or variables: BiocFileCache Consequence genes genome pancan_SE project_short_name seqlengths symbol tfstart * 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 ... NOTE Note: found 46 marked UTF-8 strings * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocOncoTK.Rcheck/00check.log' for details.
BiocOncoTK.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BiocOncoTK_1.2.1.tar.gz && rm -rf BiocOncoTK.buildbin-libdir && mkdir BiocOncoTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocOncoTK.buildbin-libdir BiocOncoTK_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BiocOncoTK_1.2.1.zip && rm BiocOncoTK_1.2.1.tar.gz BiocOncoTK_1.2.1.zip
###
##############################################################################
##############################################################################
% 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 2218k 100 2218k 0 0 35.3M 0 --:--:-- --:--:-- --:--:-- 37.3M
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'BiocOncoTK/vignettes/microsatpan.png' to 'BiocOncoTK/microsatpan.png'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'BiocOncoTK/vignettes/pancanApp.png' to 'BiocOncoTK/pancanApp.png'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'BiocOncoTK/vignettes/BiocOncoTK.Rmd' to 'BiocOncoTK/README.md'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'BiocOncoTK' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BiocOncoTK'
finding HTML links ... done
CCLE_DRUG_BROAD html
TcgaMutCounts html
TcgaNIndWithAnyMut html
annotTabs html
bindMSI html
brcaMAE html
buildPancanSE html
cell_70138 html
clueDemos html
clueServiceNames html
darmGBMcls html
dingMSI html
fireMSI html
ggFeatDens html
ggFeatureSegs html
ggMutDens html
icd10_c html
loadPatel html
mc3toGR html
oncoPrintISB html
pancan.clin.varnames html
pancan_BQ html
finding level-2 HTML links ... done
pancan_app html
pancan_clinicalTabVarnames html
pancan_longname html
pancan_sampTypeMap html
pancan_tabulate html
pertClasses html
pert_70138 html
query_clue html
replaceRownames html
tumNorSet html
utils html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'BiocOncoTK/vignettes/microsatpan.png' to 'BiocOncoTK/microsatpan.png'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'BiocOncoTK/vignettes/pancanApp.png' to 'BiocOncoTK/pancanApp.png'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'BiocOncoTK/vignettes/BiocOncoTK.Rmd' to 'BiocOncoTK/README.md'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'BiocOncoTK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocOncoTK' as BiocOncoTK_1.2.1.zip
* DONE (BiocOncoTK)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BiocOncoTK' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
BiocOncoTK.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # authentication is so problematic that I am skipping this for now
> library(testthat)
> library(BiocOncoTK)
> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
> library(reshape2)
>
> #test_check("BiocOncoTK")
>
> proc.time()
user system elapsed
6.67 0.31 7.06
|
BiocOncoTK.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # authentication is so problematic that I am skipping this for now
> library(testthat)
> library(BiocOncoTK)
> library(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
> library(reshape2)
>
> #test_check("BiocOncoTK")
>
> proc.time()
user system elapsed
6.79 0.34 7.12
|
|
BiocOncoTK.Rcheck/examples_i386/BiocOncoTK-Ex.timings
|
BiocOncoTK.Rcheck/examples_x64/BiocOncoTK-Ex.timings
|