Luyue Wang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/LinTInd |
| git_branch: master |
| git_last_commit: 1604c96 |
| git_last_commit_date: 2022-02-07 06:30:36 -0400 (Mon, 07 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:53 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1005/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LinTInd 0.99.5 (landing page) Luyue Wang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 0.99.5 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LinTInd.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings LinTInd_0.99.5.tar.gz |
| StartedAt: 2022-03-17 19:26:48 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:28:46 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 118.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LinTInd.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LinTInd.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings LinTInd_0.99.5.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/LinTInd.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LinTInd/DESCRIPTION' ... OK
* this is package 'LinTInd' version '0.99.5'
* 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 ... 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 0.08 0.01 11.14
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/LinTInd.Rcheck/00check.log'
for details.
LinTInd.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL LinTInd
###
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* installing to library 'D:/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
converting help for package 'LinTInd'
finding HTML links ... done
BuildTree html
FindIndel html
IndelForm html
IndelIdents html
IndelPlot html
PlotTree html
ReadCutsite html
ReadFasta html
TagDist html
TagProcess html
align_to_range html
cellsinfo html
celltype html
change_form_stat html
cutsite html
data html
example_data html
ref html
scarform html
scarinfo html
scarref html
scarref_all html
tag html
treeinfo html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'surfaltr' is missing or broken
done
LinTInd.Rcheck/LinTInd-Ex.timings
| name | user | system | elapsed | |
| BuildTree | 0.06 | 0.00 | 0.60 | |
| FindIndel | 0.08 | 0.01 | 11.14 | |
| IndelForm | 0.23 | 0.02 | 4.80 | |
| IndelIdents | 0.10 | 0.05 | 3.59 | |
| IndelPlot | 1.03 | 0.01 | 1.05 | |
| PlotTree | 0.39 | 0.00 | 0.40 | |
| ReadCutsite | 0.00 | 0.02 | 0.02 | |
| ReadFasta | 0.25 | 0.00 | 0.25 | |
| TagDist | 2.09 | 0.08 | 2.17 | |
| TagProcess | 0.02 | 0.01 | 0.03 | |
| align_to_range | 0 | 0 | 0 | |
| change_form_stat | 0.01 | 0.00 | 0.02 | |
| example_data | 0 | 0 | 0 | |