Luyue Wang
| Snapshot Date: 2025-05-08 13:00 -0400 (Thu, 08 May 2025) |
| git_url: https://git.bioconductor.org/packages/LinTInd |
| git_branch: devel |
| git_last_commit: 1287ca4 |
| git_last_commit_date: 2025-04-15 12:45:30 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-05-09 12:07 -0400 (Fri, 09 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4749 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4510 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4489 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4449 |
| 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 1116/2304 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LinTInd 1.13.0 (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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.13.0 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LinTInd.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings LinTInd_1.13.0.tar.gz |
| StartedAt: 2025-05-09 03:10:43 -0400 (Fri, 09 May 2025) |
| EndedAt: 2025-05-09 03:13:34 -0400 (Fri, 09 May 2025) |
| EllapsedTime: 171.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LinTInd.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LinTInd.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings LinTInd_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/LinTInd.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'LinTInd/DESCRIPTION' ... OK
* this is package 'LinTInd' version '1.13.0'
* 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 '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
IndelForm 0.38 0.10 6.30
IndelIdents 0.17 0.03 6.18
FindIndel 0.16 0.03 14.20
* 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
'F:/biocbuild/bbs-3.22-bioc/meat/LinTInd.Rcheck/00check.log'
for details.
LinTInd.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL LinTInd ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'LinTInd' ... ** this is package 'LinTInd' version '1.13.0' ** 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 | 0.14 | 0.06 | 0.77 | |
| FindIndel | 0.16 | 0.03 | 14.20 | |
| IndelForm | 0.38 | 0.10 | 6.30 | |
| IndelIdents | 0.17 | 0.03 | 6.18 | |
| IndelPlot | 1.92 | 0.01 | 1.95 | |
| PlotTree | 0.69 | 0.00 | 0.78 | |
| ReadCutsite | 0.01 | 0.00 | 0.02 | |
| ReadFasta | 0.02 | 0.00 | 0.01 | |
| TagDist | 4.39 | 0.13 | 4.82 | |
| TagProcess | 0.05 | 0.00 | 0.04 | |
| align_to_range | 0.01 | 0.00 | 0.02 | |
| change_form_stat | 0.02 | 0.00 | 0.02 | |
| example_data | 0 | 0 | 0 | |