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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1116/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LinTInd 1.8.0  (landing page)
Luyue Wang
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/LinTInd
git_branch: RELEASE_3_19
git_last_commit: 4f54123
git_last_commit_date: 2024-04-30 11:40:13 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for LinTInd on kjohnson3

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.

raw results


Summary

Package: LinTInd
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-06-10 20:08:53 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 20:12:24 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 211.3 seconds
RetCode: 0
Status:   OK  
CheckDir: LinTInd.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/LinTInd.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LinTInd/DESCRIPTION’ ... OK
* this is package ‘LinTInd’ version ‘1.8.0’
* 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     3.993  0.161   5.303
IndelForm   0.371  0.055   7.774
IndelIdents 0.179  0.034   7.273
FindIndel   0.098  0.023  16.290
* 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-3.19-bioc/meat/LinTInd.Rcheck/00check.log’
for details.


Installation output

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-arm64/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)

Tests output


Example timings

LinTInd.Rcheck/LinTInd-Ex.timings

nameusersystemelapsed
BuildTree0.1910.1160.571
FindIndel 0.098 0.02316.290
IndelForm0.3710.0557.774
IndelIdents0.1790.0347.273
IndelPlot1.6160.0212.170
PlotTree0.5420.0100.707
ReadCutsite0.0070.0050.018
ReadFasta0.0060.0010.010
TagDist3.9930.1615.303
TagProcess0.0350.0060.049
align_to_range0.0110.0010.017
change_form_stat0.0160.0020.025
example_data0.0010.0010.002