| 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 genomicInstability package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomicInstability.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 753/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genomicInstability 1.0.0 (landing page) Mariano Alvarez
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: genomicInstability |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genomicInstability.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings genomicInstability_1.0.0.tar.gz |
| StartedAt: 2022-04-12 20:14:22 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:18:07 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 224.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: genomicInstability.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:genomicInstability.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings genomicInstability_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/genomicInstability.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 'genomicInstability/DESCRIPTION' ... OK
* this is package 'genomicInstability' version '1.0.0'
* 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 'genomicInstability' 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
mixGaussianFit : <anonymous>: warning in normalmixEM(x, lambda =
param$lambda, mu = param$m, sd = param$sigma, epsilon = 1e-50):
partial argument match of 'sd' to 'sd.constr'
aecdf1: no visible global function definition for 'quantile'
aecdf1: no visible global function definition for 'ecdf'
aecdf1: no visible binding for global variable 'tl2'
aecdf1: no visible binding for global variable 'iq2'
aecdf1: no visible global function definition for 'epd'
aecdf1: no visible global function definition for 'lm'
aecdf1: no visible global function definition for 'predict'
aecdf1: no visible global function definition for 'qnorm'
colorScale: no visible global function definition for 'col2rgb'
colorScale : <anonymous>: no visible global function definition for
'rgb'
generateChromosomeGeneSet: no visible global function definition for
'data'
generateChromosomeGeneSet: no visible binding for global variable
'hg38'
generateChromosomeGeneSet: no visible binding for global variable
'mm10'
generateChromosomeGeneSet: no visible binding for global variable
'genePosition'
getPeaks: no visible global function definition for 'density'
getPeaks3: no visible global function definition for 'density'
getPeaks3: no visible global function definition for 'smooth.spline'
getPeaks3: no visible global function definition for 'predict'
getPeaks3 : <anonymous>: no visible global function definition for
'approx'
giDensityPlot: no visible global function definition for 'density'
giDensityPlot: no visible global function definition for 'lines'
giLikelihood: no visible global function definition for 'sd'
giLikelihood: no visible global function definition for 'predict'
mixGaussianFit : <anonymous> : <anonymous>: no visible global function
definition for 'dnorm'
mixGaussianFit: no visible global function definition for 'density'
plot.inferCNV: no visible global function definition for 'pdf'
plot.inferCNV: no visible global function definition for 'png'
plot.inferCNV: no visible global function definition for 'jpeg'
plot.inferCNV: no visible global function definition for 'layout'
plot.inferCNV: no visible global function definition for 'par'
plot.inferCNV: no visible global function definition for 'axis'
plot.inferCNV: no visible global function definition for 'dev.off'
plot.mgfit: no visible global function definition for 'rainbow'
plot.mgfit: no visible global function definition for 'density'
plot.mgfit: no visible global function definition for 'dnorm'
plot.mgfit: no visible global function definition for 'axis'
plot.mgfit: no visible global function definition for 'polygon'
plot.mgfit: no visible global function definition for 'lines'
plothm: no visible global function definition for 'par'
plothm: no visible global function definition for 'layout'
plothm: no visible global function definition for 'axis'
plothm: no visible global function definition for 'image'
plothm.: no visible global function definition for 'image'
predict.mgfit : <anonymous>: no visible global function definition for
'dnorm'
sREA: no visible global function definition for 'qnorm'
sortRowsByHclust: no visible global function definition for 'dist'
sortRowsByHclust: no visible global function definition for 'hclust'
Undefined global functions or variables:
approx axis col2rgb data density dev.off dist dnorm ecdf epd
genePosition hclust hg38 image iq2 jpeg layout lines lm mm10 par pdf
png polygon predict qnorm quantile rainbow rgb sd smooth.spline tl2
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
"rainbow", "rgb")
importFrom("graphics", "axis", "image", "layout", "lines", "par",
"polygon")
importFrom("stats", "approx", "density", "dist", "dnorm", "ecdf",
"hclust", "lm", "predict", "qnorm", "quantile", "sd",
"smooth.spline")
importFrom("utils", "data")
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' ... ERROR
Running examples in 'genomicInstability-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomicInstabilityScore
> ### Title: Genomic Instability Analysis
> ### Aliases: genomicInstabilityScore
>
> ### ** Examples
>
>
> eh <- ExperimentHub::ExperimentHub()
snapshotDate(): 2021-10-19
> dset <- eh[["EH5419"]]
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing package(s) 'GSE103322'
Error in UseMethod("conditionMessage") :
no applicable method for 'conditionMessage' applied to an object of class "character"
Calls: [[ ... tryCatchList -> tryCatchOne -> doTryCatch -> download.file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'genomicInstability-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomicInstabilityScore
> ### Title: Genomic Instability Analysis
> ### Aliases: genomicInstabilityScore
>
> ### ** Examples
>
>
> eh <- ExperimentHub::ExperimentHub()
snapshotDate(): 2021-10-19
> dset <- eh[["EH5419"]]
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing package(s) 'GSE103322'
Error in UseMethod("conditionMessage") :
no applicable method for 'conditionMessage' applied to an object of class "character"
Calls: [[ ... tryCatchList -> tryCatchOne -> doTryCatch -> download.file
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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/genomicInstability.Rcheck/00check.log'
for details.
genomicInstability.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/genomicInstability_1.0.0.tar.gz && rm -rf genomicInstability.buildbin-libdir && mkdir genomicInstability.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genomicInstability.buildbin-libdir genomicInstability_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL genomicInstability_1.0.0.zip && rm genomicInstability_1.0.0.tar.gz genomicInstability_1.0.0.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
37 407k 37 152k 0 0 666k 0 --:--:-- --:--:-- --:--:-- 666k
100 407k 100 407k 0 0 1077k 0 --:--:-- --:--:-- --:--:-- 1077k
install for i386
* installing *source* package 'genomicInstability' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'genomicInstability'
finding HTML links ... done
geneLength html
genePosition html
generateChromosomeGeneSet html
genomicInstability-package html
genomicInstabilityScore html
giDensityPlot html
giLikelihood html
inferCNV html
plot.inferCNV 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 'genomicInstability' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomicInstability' as genomicInstability_1.0.0.zip
* DONE (genomicInstability)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'genomicInstability' successfully unpacked and MD5 sums checked
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genomicInstability.Rcheck/examples_i386/genomicInstability-Ex.timings
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genomicInstability.Rcheck/examples_x64/genomicInstability-Ex.timings
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