Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1108/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LinTInd 1.10.0 (landing page) Luyue Wang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the LinTInd package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LinTInd.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: LinTInd |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LinTInd_1.10.0.tar.gz |
StartedAt: 2024-12-20 05:17:49 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:22:31 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 281.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LinTInd.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LinTInd_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/LinTInd.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘LinTInd/DESCRIPTION’ ... OK * this is package ‘LinTInd’ version ‘1.10.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘LinTInd’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 BuildTree: no visible global function definition for ‘write.csv’ FindIndel : find_barcode: no visible global function definition for ‘is’ FindIndel: no visible global function definition for ‘write.table’ IndelForm: no visible global function definition for ‘write.csv’ IndelIdents: no visible global function definition for ‘write.csv’ IndelIdents : max_reads_stat: no visible global function definition for ‘is’ IndelPlot: no visible binding for global variable ‘Site’ IndelPlot: no visible binding for global variable ‘Freq’ PlotTree: no visible binding for global variable ‘tags’ PlotTree: no visible binding for global variable ‘celltype’ PlotTree: no visible binding for global variable ‘Freq’ PlotTree : SortTree: no visible binding for global variable ‘tag_number’ PlotTree: no visible binding for global variable ‘y’ PlotTree: no visible binding for global variable ‘variable’ PlotTree: no visible binding for global variable ‘value’ ReadFasta: no visible global function definition for ‘read.table’ TagProcess: no visible binding for global variable ‘i’ change_form_stat : <anonymous>: no visible binding for global variable ‘scarref’ change_form_stat: no visible binding for global variable ‘scarref’ Undefined global functions or variables: Freq Site celltype i is read.table scarref tag_number tags value variable write.csv write.table y Consider adding importFrom("methods", "is") importFrom("utils", "read.table", "write.csv", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: cellsinfo.Rd:10: Dropping empty section \source prepare_Rd: cellsinfo.Rd:11-12: Dropping empty section \references prepare_Rd: celltype.Rd:10: Dropping empty section \source prepare_Rd: celltype.Rd:11-12: Dropping empty section \references prepare_Rd: cutsite.Rd:10: Dropping empty section \source prepare_Rd: cutsite.Rd:11-12: Dropping empty section \references prepare_Rd: data.Rd:10: Dropping empty section \source prepare_Rd: data.Rd:11-12: Dropping empty section \references prepare_Rd: example_data.Rd:15-17: Dropping empty section \details prepare_Rd: example_data.Rd:18-20: Dropping empty section \source prepare_Rd: example_data.Rd:21-23: Dropping empty section \references prepare_Rd: ref.Rd:10: Dropping empty section \source prepare_Rd: ref.Rd:11-12: Dropping empty section \references prepare_Rd: scarform.Rd:10: Dropping empty section \source prepare_Rd: scarform.Rd:11-12: Dropping empty section \references prepare_Rd: scarinfo.Rd:10: Dropping empty section \source prepare_Rd: scarinfo.Rd:11-12: Dropping empty section \references prepare_Rd: scarref.Rd:10: Dropping empty section \source prepare_Rd: scarref.Rd:11-12: Dropping empty section \references prepare_Rd: scarref_all.Rd:10: Dropping empty section \source prepare_Rd: scarref_all.Rd:11-12: Dropping empty section \references prepare_Rd: tag.Rd:10: Dropping empty section \source prepare_Rd: tag.Rd:11-12: Dropping empty section \references prepare_Rd: treeinfo.Rd:10: Dropping empty section \source prepare_Rd: treeinfo.Rd:11-12: Dropping empty section \references * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TagDist 8.736 0.125 9.706 IndelForm 0.726 0.139 11.260 IndelIdents 0.313 0.095 10.481 FindIndel 0.174 0.034 27.914 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/LinTInd.Rcheck/00check.log’ for details.
LinTInd.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LinTInd ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘LinTInd’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." [1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead." [1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead." ** 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 (LinTInd)
LinTInd.Rcheck/LinTInd-Ex.timings
name | user | system | elapsed | |
BuildTree | 0.331 | 0.111 | 0.582 | |
FindIndel | 0.174 | 0.034 | 27.914 | |
IndelForm | 0.726 | 0.139 | 11.260 | |
IndelIdents | 0.313 | 0.095 | 10.481 | |
IndelPlot | 3.462 | 0.025 | 3.730 | |
PlotTree | 1.097 | 0.012 | 1.211 | |
ReadCutsite | 0.017 | 0.033 | 0.052 | |
ReadFasta | 0.008 | 0.002 | 0.010 | |
TagDist | 8.736 | 0.125 | 9.706 | |
TagProcess | 0.080 | 0.012 | 0.093 | |
align_to_range | 0.018 | 0.001 | 0.018 | |
change_form_stat | 0.026 | 0.002 | 0.028 | |
example_data | 0.002 | 0.001 | 0.004 | |