Mikhail Dozmorov
| Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/TADCompare |
| git_branch: RELEASE_3_21 |
| git_last_commit: 5868ee6 |
| git_last_commit_date: 2025-04-15 11:59:09 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 2157/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TADCompare 1.18.0 (landing page) Mikhail Dozmorov
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the TADCompare package: - 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 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: TADCompare |
| Version: 1.18.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TADCompare.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings TADCompare_1.18.0.tar.gz |
| StartedAt: 2025-08-15 07:42:02 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 07:45:59 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 236.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TADCompare.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TADCompare.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings TADCompare_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/TADCompare.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TADCompare/DESCRIPTION' ... OK
* this is package 'TADCompare' version '1.18.0'
* 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 ... 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
.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 ... 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
'E:/biocbuild/bbs-3.21-bioc/meat/TADCompare.Rcheck/00check.log'
for details.
TADCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL TADCompare ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'TADCompare' ... ** this is package 'TADCompare' version '1.18.0' ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (TADCompare)
TADCompare.Rcheck/TADCompare-Ex.timings
| name | user | system | elapsed | |
| ConsensusTADs | 2.17 | 0.07 | 2.25 | |
| DiffPlot | 1.61 | 0.13 | 1.74 | |
| TADCompare | 0.17 | 0.03 | 0.21 | |
| TimeCompare | 1.22 | 0.13 | 1.34 | |