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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).
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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 1891/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TADCompare 1.2.0 (landing page) Kellen Cresswell
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TADCompare |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TADCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TADCompare_1.2.0.tar.gz |
| StartedAt: 2021-10-15 06:26:33 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:31:13 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 280.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TADCompare.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TADCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TADCompare_1.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TADCompare.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.2.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/TADCompare.Rcheck/00check.log'
for details.
TADCompare.Rcheck/00install.out
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TADCompare_1.2.0.tar.gz && rm -rf TADCompare.buildbin-libdir && mkdir TADCompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TADCompare.buildbin-libdir TADCompare_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TADCompare_1.2.0.zip && rm TADCompare_1.2.0.tar.gz TADCompare_1.2.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2525k 100 2525k 0 0 2595k 0 --:--:-- --:--:-- --:--:-- 2598k
install for i386
* 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
install for x64
* installing *source* package 'TADCompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TADCompare' as TADCompare_1.2.0.zip
* DONE (TADCompare)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TADCompare' successfully unpacked and MD5 sums checked
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TADCompare.Rcheck/examples_i386/TADCompare-Ex.timings
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TADCompare.Rcheck/examples_x64/TADCompare-Ex.timings
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