Jack Fu
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/ballgown |
| git_branch: RELEASE_3_14 |
| git_last_commit: 4f1dda8 |
| git_last_commit_date: 2021-10-26 12:14:54 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:11 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 109/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ballgown 2.26.0 (landing page) Jack Fu
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ballgown |
| Version: 2.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ballgown.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ballgown_2.26.0.tar.gz |
| StartedAt: 2022-04-12 15:52:28 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:04:07 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 699.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ballgown.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ballgown.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ballgown_2.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ballgown.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.26.0'
* 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 20.93 0.29 21.42
contains 9.79 0.02 9.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotate_assembly 22.83 0.08 22.91
contains 11.99 0.01 12.00
* 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-3.14-bioc/meat/ballgown.Rcheck/00check.log'
for details.
ballgown.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ballgown_2.26.0.tar.gz && rm -rf ballgown.buildbin-libdir && mkdir ballgown.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ballgown.buildbin-libdir ballgown_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ballgown_2.26.0.zip && rm ballgown_2.26.0.tar.gz ballgown_2.26.0.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
2 3349k 2 99k 0 0 515k 0 0:00:06 --:--:-- 0:00:06 515k
56 3349k 56 1881k 0 0 1574k 0 0:00:02 0:00:01 0:00:01 1574k
100 3349k 100 3349k 0 0 1874k 0 0:00:01 0:00:01 --:--:-- 1874k
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-3.14-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
expr html
exprfilter html
geneIDs html
geneNames html
getAttributeField html
getGenes html
gexpr html
gffRead html
gffReadGR html
iexpr html
indexes-replace html
indexes html
last html
mergedDate html
pData-replace html
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_2.26.0.zip
* DONE (ballgown)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ballgown' successfully unpacked and MD5 sums checked
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ballgown.Rcheck/tests_i386/test-all.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
>
> proc.time()
user system elapsed
86.14 1.73 87.86
|
ballgown.Rcheck/tests_x64/test-all.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
>
> proc.time()
user system elapsed
98.45 0.87 99.32
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ballgown.Rcheck/examples_i386/ballgown-Ex.timings
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ballgown.Rcheck/examples_x64/ballgown-Ex.timings
|