Luyue Wang
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/LinTInd |
| git_branch: RELEASE_3_15 |
| git_last_commit: f035997 |
| git_last_commit_date: 2022-04-26 12:21:10 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:27 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the LinTInd package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1027/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LinTInd 1.0.0 (landing page) Luyue Wang
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: LinTInd |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings LinTInd_1.0.0.tar.gz |
| StartedAt: 2022-10-18 20:19:59 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 20:21:53 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 114.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LinTInd.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings LinTInd_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/LinTInd.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LinTInd/DESCRIPTION’ ... OK
* this is package ‘LinTInd’ version ‘1.0.0’
* 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 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 0.124 0.004 10.202
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.15-bioc/meat/LinTInd.Rcheck/00check.log’
for details.
LinTInd.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL LinTInd ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 | 0.112 | 0.030 | 0.149 | |
| FindIndel | 0.124 | 0.004 | 10.202 | |
| IndelForm | 0.297 | 0.064 | 4.341 | |
| IndelIdents | 0.137 | 0.041 | 4.317 | |
| IndelPlot | 1.241 | 0.000 | 1.241 | |
| PlotTree | 0.354 | 0.020 | 0.374 | |
| ReadCutsite | 0.004 | 0.011 | 0.016 | |
| ReadFasta | 0.005 | 0.000 | 0.006 | |
| TagDist | 2.999 | 0.124 | 3.123 | |
| TagProcess | 0.026 | 0.008 | 0.033 | |
| align_to_range | 0.009 | 0.000 | 0.008 | |
| change_form_stat | 0.010 | 0.004 | 0.014 | |
| example_data | 0.001 | 0.000 | 0.001 | |