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CHECK report for BiocOncoTK on tokay2

This page was generated on 2019-07-22 12:23:34 -0400 (Mon, 22 Jul 2019).

Package 148/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.4.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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###
### Running 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
###
##############################################################################
##############################################################################


* 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.



Installation output

BiocOncoTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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

Tests output

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 

Example timings

BiocOncoTK.Rcheck/examples_i386/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.080.020.09
TcgaMutCounts000
TcgaNIndWithAnyMut000
annotTabs000
bindMSI000
brcaMAE1.760.061.82
buildPancanSE000
cell_701380.000.020.02
clueDemos000
clueServiceNames000
darmGBMcls0.250.040.30
dingMSI0.020.000.01
featIDMapper000
fireMSI1.060.272.91
ggFeatDens000
ggFeatureSegs000
ggMutDens000
icd10_c0.030.000.03
loadPatel000
mc3toGR000
oncoPrintISB000
pancan.clin.varnames0.020.000.01
pancan_BQ000
pancan_app000
pancan_clinicalTabVarnames000
pancan_longname0.00.02.8
pancan_sampTypeMap000
pancan_tabulate000
pertClasses000
pert_70138000
query_clue000
tumNorSet000
utils 1.00 0.1412.31

BiocOncoTK.Rcheck/examples_x64/BiocOncoTK-Ex.timings

nameusersystemelapsed
CCLE_DRUG_BROAD0.100.000.09
TcgaMutCounts000
TcgaNIndWithAnyMut000
annotTabs0.000.010.02
bindMSI000
brcaMAE1.650.021.69
buildPancanSE000
cell_701380.000.010.01
clueDemos000
clueServiceNames000
darmGBMcls0.450.050.50
dingMSI0.040.000.03
featIDMapper000
fireMSI1.650.021.68
ggFeatDens000
ggFeatureSegs000
ggMutDens000
icd10_c0.030.000.03
loadPatel000
mc3toGR000
oncoPrintISB000
pancan.clin.varnames000
pancan_BQ000
pancan_app000
pancan_clinicalTabVarnames000
pancan_longname000
pancan_sampTypeMap0.020.000.01
pancan_tabulate000
pertClasses000
pert_70138000
query_clue000
tumNorSet000
utils0.640.060.71