VJ Carey
| Snapshot Date: 2019-07-21 17:01:33 -0400 (Sun, 21 Jul 2019) |
| URL: https://git.bioconductor.org/packages/BiocOncoTK |
| Branch: RELEASE_3_9 |
| Last Commit: 2cd2204 |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-07-22 12:23:34 -0400 (Mon, 22 Jul 2019).
| Package 148/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocOncoTK 1.4.0 VJ Carey
| 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 | |
| Package: BiocOncoTK |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocOncoTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiocOncoTK_1.4.0.tar.gz |
| StartedAt: 2019-07-22 02:01:32 -0400 (Mon, 22 Jul 2019) |
| EndedAt: 2019-07-22 02:06:26 -0400 (Mon, 22 Jul 2019) |
| EllapsedTime: 293.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocOncoTK.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:BiocOncoTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiocOncoTK_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck'
* using R version 3.6.0 (2019-04-26)
* 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 '1.4.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'BiocOncoTK' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpU765wh/R.INSTALL25984dd05d59/BiocOncoTK/man/reexports.Rd:19: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Found the following additional notes/warnings:
Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 3.9Mb
pamphlets 4.5Mb
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
utils 1 0.14 12.31
** 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocOncoTK.Rcheck/00check.log'
for details.
BiocOncoTK.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/BiocOncoTK_1.4.0.tar.gz && rm -rf BiocOncoTK.buildbin-libdir && mkdir BiocOncoTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocOncoTK.buildbin-libdir BiocOncoTK_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BiocOncoTK_1.4.0.zip && rm BiocOncoTK_1.4.0.tar.gz BiocOncoTK_1.4.0.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 6991k 100 6991k 0 0 13.8M 0 --:--:-- --:--:-- --:--:-- 14.0M
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'BiocOncoTK' ...
** using staged installation
** 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
featIDMapper 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
reexports html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpU765wh/R.INSTALL25984dd05d59/BiocOncoTK/man/reexports.Rd:19: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
replaceRownames html
tumNorSet html
utils 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) :
restoring symbolic link as a file copy
* installing *source* package 'BiocOncoTK' ...
** using non-staged installation
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocOncoTK' as BiocOncoTK_1.4.0.zip
* DONE (BiocOncoTK)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BiocOncoTK' successfully unpacked and MD5 sums checked
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BiocOncoTK.Rcheck/tests_i386/testthat.Rout
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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)
Attaching package: 'BiocOncoTK'
The following object is masked from 'package:stats':
filter
> 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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, rowsum
> library(reshape2)
>
> #test_check("BiocOncoTK")
>
> proc.time()
user system elapsed
7.09 0.68 16.06
|
BiocOncoTK.Rcheck/tests_x64/testthat.Rout
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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)
Attaching package: 'BiocOncoTK'
The following object is masked from 'package:stats':
filter
> 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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, rowsum
> library(reshape2)
>
> #test_check("BiocOncoTK")
>
> proc.time()
user system elapsed
8.31 0.46 8.76
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BiocOncoTK.Rcheck/examples_i386/BiocOncoTK-Ex.timings
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BiocOncoTK.Rcheck/examples_x64/BiocOncoTK-Ex.timings
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