Kellen Cresswell
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/TADCompare |
| git_branch: master |
| git_last_commit: 03142c5 |
| git_last_commit_date: 2021-10-26 13:00:00 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:50 -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 TADCompare package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TADCompare.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 1932/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TADCompare 1.5.0 (landing page) Kellen Cresswell
| 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: TADCompare |
| Version: 1.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TADCompare.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TADCompare_1.5.0.tar.gz |
| StartedAt: 2022-03-17 20:27:01 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:29:56 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 174.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TADCompare.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:TADCompare.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TADCompare_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TADCompare.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 'TADCompare/DESCRIPTION' ... OK
* this is package 'TADCompare' version '1.5.0'
* 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 'TADCompare' 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 ... NOTE
Namespaces in Imports field not imported from:
'Matrix' 'cluster'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Make_Triangles: no visible binding for global variable 'start'
.Make_Triangles: no visible binding for global variable 'end'
.Make_Triangles: no visible global function definition for 'na.omit'
.Make_Triangles: no visible binding for global variable
'boundary_start'
.Make_Triangles: no visible binding for global variable 'orig_regx'
.Make_Triangles: no visible binding for global variable 'start1'
.Make_Triangles: no visible binding for global variable 'boundary_end'
ConsensusTADs : <anonymous>: no visible binding for global variable
'Coordinate'
ConsensusTADs: no visible binding for global variable 'Sample'
ConsensusTADs: no visible binding for global variable 'Boundary'
ConsensusTADs: no visible binding for global variable 'Diff_Score'
ConsensusTADs: no visible global function definition for 'sd'
ConsensusTADs: no visible binding for global variable 'Differential'
ConsensusTADs: no visible binding for global variable 'Coordinate'
ConsensusTADs: no visible binding for global variable 'TAD_Score'
ConsensusTADs: no visible binding for global variable '.'
ConsensusTADs: no visible binding for global variable 'median'
DiffPlot: no visible binding for global variable 'Type'
DiffPlot: no visible binding for global variable 'Differential'
DiffPlot: no visible binding for global variable 'Boundary'
DiffPlot: no visible binding for global variable 'Enriched_In'
DiffPlot: no visible global function definition for 'na.omit'
DiffPlot: no visible binding for global variable 'boundary_start'
DiffPlot: no visible binding for global variable 'orig_regx'
DiffPlot: no visible binding for global variable 'start1'
DiffPlot: no visible binding for global variable 'boundary_end'
DiffPlot: no visible binding for global variable 'start2'
DiffPlot: no visible binding for global variable 'TAD_Score1'
DiffPlot: no visible binding for global variable 'TAD_Score2'
DiffPlot: no visible binding for global variable 'Gap_Score'
DiffPlot: no visible binding for global variable 'variable'
DiffPlot: no visible binding for global variable 'value'
DiffPlot: no visible binding for global variable 'line_spot'
DiffPlot: no visible global function definition for 'complete.cases'
DiffPlot: no visible binding for global variable '.'
DiffPlot: no visible binding for global variable 'x'
DiffPlot: no visible binding for global variable 'y'
DiffPlot: no visible binding for global variable 'orig_regy'
TADCompare: no visible global function definition for 'sd'
TADCompare: no visible binding for global variable 'Boundary'
TADCompare: no visible binding for global variable 'Gap_Score'
TADCompare: no visible binding for global variable 'Differential'
TADCompare: no visible binding for global variable 'Bound_Dist'
TADCompare: no visible binding for global variable 'Enriched_In'
TADCompare: no visible binding for global variable 'Type'
TADCompare: no visible binding for global variable 'Count'
TimeCompare : <anonymous>: no visible binding for global variable
'Coordinate'
TimeCompare: no visible binding for global variable 'Sample'
TimeCompare: no visible binding for global variable 'Groups'
TimeCompare: no visible binding for global variable 'Coordinate'
TimeCompare: no visible binding for global variable 'Boundary'
TimeCompare: no visible global function definition for 'median'
TimeCompare: no visible binding for global variable 'Diff_Score'
TimeCompare: no visible global function definition for 'sd'
TimeCompare: no visible binding for global variable 'Differential'
TimeCompare: no visible binding for global variable 'TAD_Score'
TimeCompare: no visible binding for global variable '.'
TimeCompare: no visible binding for global variable 'median'
TimeCompare: no visible binding for global variable 'Sample 1'
TimeCompare: no visible binding for global variable 'Consensus_Score'
TimeCompare: no visible binding for global variable 'Category'
TimeCompare: no visible binding for global variable 'Count'
Undefined global functions or variables:
. Bound_Dist Boundary Category Consensus_Score Coordinate Count
Diff_Score Differential Enriched_In Gap_Score Groups Sample Sample 1
TAD_Score TAD_Score1 TAD_Score2 Type boundary_end boundary_start
complete.cases end line_spot median na.omit orig_regx orig_regy sd
start start1 start2 value variable x y
Consider adding
importFrom("stats", "complete.cases", "end", "median", "na.omit", "sd",
"start")
to your NAMESPACE file.
* checking Rd files ... OK
* 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
* 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/TADCompare.Rcheck/00check.log'
for details.
TADCompare.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TADCompare
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'TADCompare' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TADCompare'
finding HTML links ... done
ConsensusTADs html
DiffPlot html
GM12878.40kb.raw.chr2 html
IMR90.40kb.raw.chr2 html
TADCompare html
TimeCompare html
rao_chr22_prim html
rao_chr22_rep html
time_mats 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 (TADCompare)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'Nebulosa' is missing or broken
done
TADCompare.Rcheck/TADCompare-Ex.timings
| name | user | system | elapsed | |
| ConsensusTADs | 1.45 | 0.13 | 1.58 | |
| DiffPlot | 0.84 | 0.14 | 0.98 | |
| TADCompare | 0.21 | 0.02 | 0.22 | |
| TimeCompare | 1.45 | 0.12 | 1.58 | |