Luyue Wang
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/LinTInd |
| git_branch: RELEASE_3_17 |
| git_last_commit: c540418 |
| git_last_commit_date: 2023-04-25 11:35:50 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:28 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1069/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LinTInd 1.4.0 (landing page) Luyue Wang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.4.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings LinTInd_1.4.0.tar.gz |
| StartedAt: 2023-10-15 22:22:53 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:25:22 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 148.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LinTInd.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings LinTInd_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/LinTInd.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘LinTInd/DESCRIPTION’ ... OK
* this is package ‘LinTInd’ version ‘1.4.0’
* 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 ... 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
* 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 ... 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
FindIndel 0.136 0.004 10.271
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘tutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/LinTInd.Rcheck/00check.log’
for details.
LinTInd.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL LinTInd ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 | 0.160 | 0.024 | 0.200 | |
| FindIndel | 0.136 | 0.004 | 10.271 | |
| IndelForm | 0.366 | 0.052 | 4.952 | |
| IndelIdents | 0.166 | 0.008 | 4.623 | |
| IndelPlot | 1.373 | 0.044 | 1.416 | |
| PlotTree | 0.445 | 0.020 | 0.465 | |
| ReadCutsite | 0.008 | 0.008 | 0.015 | |
| ReadFasta | 0.017 | 0.000 | 0.017 | |
| TagDist | 3.080 | 0.136 | 3.216 | |
| TagProcess | 0.038 | 0.000 | 0.038 | |
| align_to_range | 0.010 | 0.000 | 0.011 | |
| change_form_stat | 0.011 | 0.004 | 0.016 | |
| example_data | 0.001 | 0.000 | 0.002 | |