Katja Hebestreit
| Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BiSeq |
| git_branch: devel |
| git_last_commit: cd005cd |
| git_last_commit_date: 2024-04-30 10:31:46 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-20 12:14 -0400 (Thu, 20 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4687 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4402 |
| 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 | ||||
| Package 221/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiSeq 1.45.0 (landing page) Katja Hebestreit
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BiSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiSeq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BiSeq |
| Version: 1.45.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiSeq_1.45.0.tar.gz |
| StartedAt: 2024-06-19 21:06:35 -0400 (Wed, 19 Jun 2024) |
| EndedAt: 2024-06-19 21:12:35 -0400 (Wed, 19 Jun 2024) |
| EllapsedTime: 359.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiSeq_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BiSeq.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.45.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Formula’
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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Formula’
All declared Imports should be used.
Package in Depends field not imported from: ‘Formula’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.betaRegression : inv.link: no visible global function definition for
‘pnorm’
.betaRegression : beta.regr: no visible global function definition for
‘as.formula’
.categorialColors: no visible global function definition for ‘colors’
.estLocCor: no visible global function definition for ‘combn’
.logisticRegression : inv.link: no visible global function definition
for ‘pnorm’
.logisticRegression : logistic.regr: no visible global function
definition for ‘lm’
.logisticRegression : logistic.regr: no visible global function
definition for ‘as.formula’
.makeVariogram: no visible global function definition for ‘qnorm’
.plotBindingSites: no visible global function definition for
‘txtProgressBar’
.plotBindingSites: no visible global function definition for
‘setTxtProgressBar’
.plotBindingSites : <anonymous>: no visible global function definition
for ‘ksmooth’
.plotBindingSites: no visible global function definition for ‘rainbow’
.plotBindingSites: no visible global function definition for ‘lines’
.plotBindingSites: no visible global function definition for ‘rgb’
.plotBindingSites: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘rgb’
.plotMeth: no visible global function definition for ‘lines’
.plotMeth: no visible global function definition for ‘legend’
.plotMethMap: no visible global function definition for
‘colorRampPalette’
.plotMethMap: no visible binding for global variable ‘heatmap’
.plotSmoothMeth: no visible global function definition for ‘rainbow’
.plotSmoothMeth: no visible global function definition for ‘lines’
.predictMeth: no visible global function definition for
‘txtProgressBar’
.predictMeth: no visible global function definition for
‘setTxtProgressBar’
.testClusters: no visible global function definition for ‘pnorm’
.trimClusters : integrand: no visible global function definition for
‘pnorm’
.trimClusters : integrand: no visible global function definition for
‘qnorm’
.trimClusters : integrand: no visible global function definition for
‘dnorm’
.trimClusters: no visible global function definition for ‘integrate’
.trimClusters: no visible global function definition for ‘pnorm’
.trimClusters: no visible global function definition for ‘qnorm’
.variogram: no visible global function definition for ‘dist’
.variogram: no visible global function definition for ‘txtProgressBar’
.variogram: no visible global function definition for
‘setTxtProgressBar’
.writeBED_BSraw: no visible global function definition for ‘colorRamp’
.writeBED_BSraw: no visible global function definition for ‘rgb’
.writeBED_BSrel: no visible global function definition for ‘colorRamp’
.writeBED_BSrel: no visible global function definition for ‘rgb’
betaRegression,formula-character-BSrel-numeric : inv.link: no visible
global function definition for ‘pnorm’
betaRegression,formula-character-BSrel-numeric : beta.regr: no visible
global function definition for ‘as.formula’
estLocCor,list: no visible global function definition for ‘combn’
logisticRegression,formula-character-BSrel-numeric : inv.link: no
visible global function definition for ‘pnorm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
visible global function definition for ‘lm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
visible global function definition for ‘as.formula’
makeVariogram,data.frame-logical-numeric-numeric: no visible global
function definition for ‘qnorm’
plotMethMap,BSrel-GRanges-factor-logical: no visible global function
definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-logical: no visible binding for global
variable ‘heatmap’
plotMethMap,BSrel-GRanges-factor-missing: no visible global function
definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-missing: no visible binding for global
variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-logical: no visible global function
definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-logical: no visible binding for
global variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-missing: no visible global function
definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-missing: no visible binding for
global variable ‘heatmap’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
definition for ‘txtProgressBar’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
definition for ‘setTxtProgressBar’
testClusters,list-numeric: no visible global function definition for
‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
definition for ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
definition for ‘qnorm’
trimClusters,list-numeric : integrand: no visible global function
definition for ‘dnorm’
trimClusters,list-numeric: no visible global function definition for
‘integrate’
trimClusters,list-numeric: no visible global function definition for
‘pnorm’
trimClusters,list-numeric: no visible global function definition for
‘qnorm’
writeBED,BSraw-character-character: no visible global function
definition for ‘colorRamp’
writeBED,BSraw-character-character: no visible global function
definition for ‘rgb’
writeBED,BSrel-character-character: no visible global function
definition for ‘colorRamp’
writeBED,BSrel-character-character: no visible global function
definition for ‘rgb’
Undefined global functions or variables:
as.formula col2rgb colorRamp colorRampPalette colors combn dist dnorm
heatmap integrate ksmooth legend lines lm pnorm qnorm rainbow rgb
setTxtProgressBar txtProgressBar
Consider adding
importFrom("grDevices", "col2rgb", "colorRamp", "colorRampPalette",
"colors", "rainbow", "rgb")
importFrom("graphics", "legend", "lines")
importFrom("stats", "as.formula", "dist", "dnorm", "heatmap",
"integrate", "ksmooth", "lm", "pnorm", "qnorm")
importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) DMRs.Rd:16: Lost braces
16 | DMRs: \code{median.p}, code{median.meth.group1},
| ^
checkRd: (-1) DMRs.Rd:17: Lost braces
17 | code{median.meth.group2}, \code{median.meth.diff}.
| ^
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
betaRegression 13.956 0.707 14.663
globalTest 11.673 0.204 11.877
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/BiSeq.Rcheck/00check.log’
for details.
BiSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BiSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BiSeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (BiSeq)
BiSeq.Rcheck/BiSeq-Ex.timings
| name | user | system | elapsed | |
| BSraw-class | 0.213 | 0.011 | 0.225 | |
| BSrel-class | 0.147 | 0.020 | 0.167 | |
| DMRs | 0.023 | 0.003 | 0.027 | |
| annotateGRanges | 0.159 | 0.021 | 0.179 | |
| betaRegression | 13.956 | 0.707 | 14.663 | |
| betaResults | 0.006 | 0.001 | 0.006 | |
| betaResultsNull | 0.003 | 0.000 | 0.003 | |
| binomLikelihoodSmooth | 0.000 | 0.002 | 0.003 | |
| clusterSites | 0.385 | 0.008 | 0.394 | |
| clusterSitesToGR | 0.421 | 0.009 | 0.429 | |
| compareTwoSamples | 3.477 | 0.184 | 3.661 | |
| covBoxplots | 0.075 | 0.000 | 0.075 | |
| covStatistics | 0.032 | 0.004 | 0.036 | |
| estLocCor | 3.395 | 0.040 | 3.459 | |
| filterByCov | 0.096 | 0.007 | 0.104 | |
| filterBySharedRegions | 0.141 | 0.004 | 0.145 | |
| findDMRs | 0.323 | 0.008 | 0.331 | |
| globalTest | 11.673 | 0.204 | 11.877 | |
| limitCov | 0.451 | 0.015 | 0.467 | |
| logisticRegression | 1.208 | 0.016 | 1.224 | |
| makeVariogram | 3.478 | 0.039 | 3.517 | |
| plotBindingSites | 1.286 | 0.005 | 1.289 | |
| plotMeth | 0.177 | 0.003 | 0.180 | |
| plotMethMap | 0.177 | 0.000 | 0.177 | |
| plotSmoothMeth | 0.119 | 0.001 | 0.119 | |
| predictMeth | 1.141 | 0.015 | 1.158 | |
| predictedMeth | 0.008 | 0.000 | 0.009 | |
| promoters | 0.046 | 0.001 | 0.046 | |
| rawToRel | 0.064 | 0.000 | 0.065 | |
| readBismark | 0.065 | 0.000 | 0.066 | |
| rrbs | 0.029 | 0.003 | 0.034 | |
| smoothVariogram | 0.049 | 0.000 | 0.050 | |
| summarizeRegions | 2.443 | 0.020 | 2.462 | |
| testClusters | 0.074 | 0.001 | 0.074 | |
| trimClusters | 0.250 | 0.015 | 0.267 | |
| vario | 0.002 | 0.000 | 0.002 | |
| writeBED | 0.183 | 0.011 | 0.195 | |