| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:37 -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 | ||||
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To the developers/maintainers of the GenVisR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.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 762/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenVisR 1.26.0 (landing page) Zachary Skidmore
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: GenVisR |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenVisR_1.26.0.tar.gz |
| StartedAt: 2022-04-12 20:21:46 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:45:00 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1394.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenVisR.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenVisR_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenVisR.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 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.26.0'
* 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 'GenVisR' 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 ... NOTE
Namespace in Imports field not imported from: 'reshape2'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setTierTwo,data.table : a: no visible binding for global variable 'tmp'
toLolliplot,GMS: no visible binding for global variable 'missingINdex'
Undefined global functions or variables:
missingINdex tmp
* 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 LazyData ... 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
Lolliplot-class 45.63 2.31 413.75
lolliplot 23.02 0.06 49.38
geneViz 8.14 0.22 8.36
genCov 7.86 0.47 8.34
cnFreq 6.50 0.18 6.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Lolliplot-class 36.81 1.03 48.87
lolliplot 16.41 0.02 28.15
geneViz 8.37 0.13 8.50
genCov 7.88 0.25 8.13
cnFreq 5.47 0.03 5.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
> test_check("GenVisR")
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
== Skipped tests ===============================================================
* On Bioconductor (54)
== Failed tests ================================================================
-- Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly --
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
> test_check("GenVisR")
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
== Skipped tests ===============================================================
* On Bioconductor (54)
== Failed tests ================================================================
-- Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly --
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenVisR.Rcheck/00check.log'
for details.
GenVisR.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/GenVisR_1.26.0.tar.gz && rm -rf GenVisR.buildbin-libdir && mkdir GenVisR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenVisR.buildbin-libdir GenVisR_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenVisR_1.26.0.zip && rm GenVisR_1.26.0.tar.gz GenVisR_1.26.0.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
36 2104k 36 761k 0 0 849k 0 0:00:02 --:--:-- 0:00:02 849k
85 2104k 85 1799k 0 0 965k 0 0:00:02 0:00:01 0:00:01 965k
100 2104k 100 2104k 0 0 1026k 0 0:00:02 0:00:02 --:--:-- 1027k
install for i386
* installing *source* package 'GenVisR' ...
** 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 'GenVisR'
finding HTML links ... done
Clinical-class html
GMS-class html
GMS_Virtual-class html
GMS_v4-class html
GenVisR html
HCC1395_Germline html
HCC1395_N html
HCC1395_T html
Lolliplot-class html
LucCNseg html
MutSpectra-class html
MutationAnnotationFormat-class html
MutationAnnotationFormat_Virtual-class
html
MutationAnnotationFormat_v1.0-class html
MutationAnnotationFormat_v2.0-class html
MutationAnnotationFormat_v2.1-class html
MutationAnnotationFormat_v2.2-class html
MutationAnnotationFormat_v2.3-class html
MutationAnnotationFormat_v2.4-class html
PIK3CA html
Rainfall-class html
SNPloci html
TvTi html
VEP-class html
VEP_Virtual-class html
VEP_v88-class html
Waterfall-class html
brcaMAF html
cnFreq html
cnSpec html
cnView html
compIdent html
covBars html
cytoGeno html
drawPlot-methods html
genCov html
geneViz html
getData-methods html
getDescription-methods html
getGrob-methods html
getHeader-methods html
getMeta-methods html
getMutation-methods html
getPath-methods html
getPosition-methods html
getSample-methods html
getVersion-methods html
hg19chr html
ideoView html
lohSpec html
lohView html
lolliplot html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenVisR.buildbin-libdir/00LOCK-GenVisR/00new/GenVisR/help/lolliplot.html
lolliplot_AA2sidechain html
lolliplot_buildMain html
waterfall html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenVisR.buildbin-libdir/00LOCK-GenVisR/00new/GenVisR/help/waterfall.html
writeData-methods 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 'GenVisR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenVisR' as GenVisR_1.26.0.zip
* DONE (GenVisR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenVisR' successfully unpacked and MD5 sums checked
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GenVisR.Rcheck/tests_i386/testthat.Rout.fail
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)
> library(GenVisR)
>
> test_check("GenVisR")
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
== Skipped tests ===============================================================
* On Bioconductor (54)
== Failed tests ================================================================
-- Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly --
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
Error: Test failures
Execution halted
|
GenVisR.Rcheck/tests_x64/testthat.Rout.fail
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)
> library(GenVisR)
>
> test_check("GenVisR")
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
== Skipped tests ===============================================================
* On Bioconductor (54)
== Failed tests ================================================================
-- Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly --
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2
[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
Error: Test failures
Execution halted
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GenVisR.Rcheck/examples_i386/GenVisR-Ex.timings
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GenVisR.Rcheck/examples_x64/GenVisR-Ex.timings
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