Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-23 15:05:57 -0400 (Fri, 23 Jul 2021).

CHECK results for ballgown on tokay2

To the developers/maintainers of the ballgown package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ballgown.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 112/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.24.0  (landing page)
Jack Fu
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/ballgown
Branch: RELEASE_3_13
Last Commit: 34829e1
Last Changed Date: 2021-05-19 12:06:23 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ballgown
Version: 2.24.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ballgown.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ballgown_2.24.0.tar.gz
StartedAt: 2021-07-22 20:01:47 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 20:15:09 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 801.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ballgown.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ballgown_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ballgown.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ballgown/DESCRIPTION' ... OK
* this is package 'ballgown' version '2.24.0'
* 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 'ballgown' can be installed ... OK
* 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 ... NOTE
.readExon: no visible global function definition for 'read.table'
.readIntron: no visible global function definition for 'read.table'
.readTranscript: no visible global function definition for 'read.table'
assessSim: no visible global function definition for 'read.table'
assessSim: no visible global function definition for 'lines'
assessSim: no visible global function definition for 'legend'
ballgown: no visible global function definition for 'read.table'
ballgownrsem: no visible global function definition for 'read.table'
ballgownrsem : <anonymous>: no visible global function definition for
  'read.table'
checkAssembledTx: no visible global function definition for 'par'
checkAssembledTx: no visible global function definition for 'polygon'
checkAssembledTx: no visible global function definition for 'lines'
checkAssembledTx: no visible global function definition for 'abline'
checkAssembledTx: no visible global function definition for 'title'
checkAssembledTx: no visible global function definition for 'axis'
closestColor: no visible global function definition for 'heat.colors'
clusterTranscripts: no visible global function definition for 'cutree'
clusterTranscripts: no visible global function definition for 'hclust'
clusterTranscripts: no visible global function definition for 'as.dist'
clusterTranscripts: no visible global function definition for 'kmeans'
gffRead: no visible global function definition for 'read.table'
plotMeans: no visible global function definition for 'par'
plotMeans: no visible global function definition for 'polygon'
plotMeans: no visible global function definition for 'lines'
plotMeans: no visible global function definition for 'heat.colors'
plotMeans: no visible global function definition for 'text'
plotMeans: no visible global function definition for 'axis'
plotTranscripts: no visible global function definition for 'par'
plotTranscripts: no visible global function definition for 'title'
plotTranscripts: no visible global function definition for 'polygon'
plotTranscripts: no visible global function definition for 'lines'
plotTranscripts: no visible global function definition for
  'heat.colors'
plotTranscripts: no visible global function definition for 'text'
plotTranscripts: no visible global function definition for 'axis'
stattest: no visible global function definition for 'model.matrix'
stattest: no visible global function definition for 'p.adjust'
writeFiles: no visible global function definition for 'write.table'
subset,ballgown: no visible binding for global variable 'i_id'
subset,ballgown: no visible binding for global variable 'e_id'
subset,ballgown: no visible binding for global variable 't_id'
Undefined global functions or variables:
  abline as.dist axis cutree e_id hclust heat.colors i_id kmeans legend
  lines model.matrix p.adjust par polygon read.table t_id text title
  write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "polygon", "text", "title")
  importFrom("stats", "as.dist", "cutree", "hclust", "kmeans",
             "model.matrix", "p.adjust")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
annotate_assembly 46.71    0.7   48.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
annotate_assembly 47.83   0.05   47.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ballgown.Rcheck/00check.log'
for details.



Installation output

ballgown.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ballgown_2.24.0.tar.gz && rm -rf ballgown.buildbin-libdir && mkdir ballgown.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ballgown.buildbin-libdir ballgown_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ballgown_2.24.0.zip && rm ballgown_2.24.0.tar.gz ballgown_2.24.0.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
 76 3218k   76 2461k    0     0  4989k      0 --:--:-- --:--:-- --:--:-- 4992k
100 3218k  100 3218k    0     0  5342k      0 --:--:-- --:--:-- --:--:-- 5345k

install for i386

* installing *source* package 'ballgown' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'structure' in package 'ballgown'
** help
*** installing help indices
  converting help for package 'ballgown'
    finding HTML links ... done
    annotate_assembly                       html  
    ballgown-class                          html  
    ballgown-constructor                    html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ballgown.buildbin-libdir/00LOCK-ballgown/00new/ballgown/help/ballgown.html
    ballgown-package                        html  
    ballgownrsem                            html  
    bg                                      html  
    checkAssembledTx                        html  
    clusterTranscripts                      html  
    collapseTranscripts                     html  
    contains                                html  
    dirs                                    html  
    eexpr                                   html  
    expr-replace                            html  
REDIRECT:topic	 expr<- -> expr-replace.html [ FAIL ]
REDIRECT:topic	 expr<-,ballgown-method -> expr-replace.html [ FAIL ]
    expr                                    html  
    exprfilter                              html  
    geneIDs                                 html  
    geneNames                               html  
    getAttributeField                       html  
    getGenes                                html  
    gexpr                                   html  
    gffRead                                 html  
    gffReadGR                               html  
    iexpr                                   html  
    indexes-replace                         html  
REDIRECT:topic	 indexes<- -> indexes-replace.html [ FAIL ]
REDIRECT:topic	 indexes<-,ballgown-method -> indexes-replace.html [ FAIL ]
    indexes                                 html  
    last                                    html  
    mergedDate                              html  
    pData-replace                           html  
REDIRECT:topic	 pData<- -> pData-replace.html [ FAIL ]
REDIRECT:topic	 pData<-,ballgown,ANY-method -> pData-replace.html [ FAIL ]
    pData                                   html  
    pctOverlap                              html  
    plotLatentTranscripts                   html  
    plotMeans                               html  
    plotTranscripts                         html  
    sampleNames                             html  
    seqnames                                html  
    stattest                                html  
    structure                               html  
    subset                                  html  
    tGene                                   html  
    texpr                                   html  
    transcriptIDs                           html  
    transcriptNames                         html  
    writeFiles                              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

* installing *source* package 'ballgown' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ballgown' as ballgown_2.24.0.zip
* DONE (ballgown)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ballgown' successfully unpacked and MD5 sums checked

Tests output

ballgown.Rcheck/tests_i386/test-all.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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.

> library(testthat)
> test_check('ballgown')
Loading required package: ballgown

Attaching package: 'ballgown'

The following object is masked from 'package:base':

    structure

[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 170.95    1.64  172.57 

ballgown.Rcheck/tests_x64/test-all.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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.

> library(testthat)
> test_check('ballgown')
Loading required package: ballgown

Attaching package: 'ballgown'

The following object is masked from 'package:base':

    structure

[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 193.95    0.68  194.67 

Example timings

ballgown.Rcheck/examples_i386/ballgown-Ex.timings

nameusersystemelapsed
annotate_assembly46.71 0.7048.83
ballgown-class0.070.000.08
ballgown-constructor0.170.090.26
ballgownrsem2.970.043.06
bg0.060.000.07
checkAssembledTx000
clusterTranscripts0.350.010.36
collapseTranscripts0.40.00.4
dirs0.050.000.05
eexpr0.050.000.05
expr-replace0.040.000.04
expr0.050.000.05
exprfilter0.090.000.09
geneIDs0.030.000.03
geneNames2.080.002.08
getAttributeField0.70.00.7
getGenes1.950.021.97
gexpr1.580.011.59
gffRead0.10.00.1
gffReadGR0.430.030.47
iexpr0.050.000.04
indexes-replace0.060.000.07
indexes0.030.020.04
last0.020.000.02
mergedDate0.030.020.05
pData-replace0.060.000.06
pData0.040.010.04
pctOverlap0.430.020.46
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.100.010.11
seqnames0.070.020.09
stattest0.160.000.16
structure0.060.010.08
subset0.220.000.21
tGene0.050.000.05
texpr0.050.000.05
transcriptIDs0.020.020.03
transcriptNames0.050.000.05
writeFiles000

ballgown.Rcheck/examples_x64/ballgown-Ex.timings

nameusersystemelapsed
annotate_assembly47.83 0.0547.87
ballgown-class0.070.000.08
ballgown-constructor0.230.010.25
ballgownrsem2.380.042.40
bg0.050.000.05
checkAssembledTx000
clusterTranscripts0.370.000.38
collapseTranscripts0.420.000.42
dirs0.030.010.05
eexpr0.020.020.03
expr-replace0.030.000.03
expr0.030.010.04
exprfilter0.080.020.10
geneIDs0.030.000.03
geneNames2.470.002.47
getAttributeField0.770.000.76
getGenes2.010.002.02
gexpr1.860.001.86
gffRead0.080.000.08
gffReadGR0.410.030.43
iexpr0.040.000.05
indexes-replace0.030.000.03
indexes0.030.000.03
last000
mergedDate0.040.000.04
pData-replace0.030.000.03
pData0.040.000.04
pctOverlap0.380.000.38
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.030.000.03
seqnames0.020.020.03
stattest0.070.000.07
structure0.070.000.07
subset0.20.00.2
tGene0.030.000.03
texpr0.030.000.03
transcriptIDs0.030.000.03
transcriptNames0.030.000.04
writeFiles000