Douglas H Phanstiel
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/Sushi |
| git_branch: master |
| git_last_commit: 04b874c |
| git_last_commit_date: 2021-11-15 13:39:09 -0400 (Mon, 15 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:49 -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 Sushi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Sushi.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 1914/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Douglas H Phanstiel
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Sushi |
| Version: 1.33.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sushi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Sushi_1.33.1.tar.gz |
| StartedAt: 2022-03-17 20:25:45 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:27:39 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 113.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Sushi.Rcheck |
| Warnings: 3 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sushi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Sushi_1.33.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Sushi.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 'Sushi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Sushi' version '1.33.1'
* 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 'Sushi' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'Sushi' is deprecated and will be removed from Bioconductor
See 'D:/biocbuild/bbs-3.15-bioc/meat/Sushi.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* 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 ... WARNING
Undocumented arguments in documentation object 'plotBedpe'
'border'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... WARNING
Warning: large data file saved inefficiently:
size ASCII compress
Sushi_5C.bedpe.rda 321Kb TRUE none
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
Sushi_5C.bedpe.rda 321Kb 62Kb xz
Sushi_ChIAPET_pol2.bedpe.rda 846Kb 451Kb xz
Sushi_ChIPExo_CTCF.bedgraph.rda 29Kb 13Kb xz
Sushi_ChIPSeq_CTCF.bedgraph.rda 160Kb 37Kb xz
Sushi_ChIPSeq_pol2.bedgraph.rda 28Kb 11Kb xz
Sushi_DNaseI.bedgraph.rda 23Kb 12Kb xz
Sushi_GWAS.bed.rda 515Kb 241Kb xz
Sushi_HiC.matrix.rda 40Kb 31Kb xz
* 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: 3 WARNINGs, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/Sushi.Rcheck/00check.log'
for details.
Sushi.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Sushi
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Sushi' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Sushi'
finding HTML links ... done
SushiColors html
Sushi_5C.bedpe html
Sushi_ChIAPET_pol2.bedpe html
Sushi_ChIPExo_CTCF.bedgraph html
Sushi_ChIPSeq_CTCF.bedgraph html
Sushi_ChIPSeq_pol2.bed html
Sushi_ChIPSeq_pol2.bedgraph html
Sushi_ChIPSeq_severalfactors.bed html
Sushi_DNaseI.bedgraph html
Sushi_GWAS.bed html
Sushi_HiC.matrix html
Sushi_RNASeq_K562.bedgraph html
Sushi_genes.bed html
Sushi_hg18_genome html
Sushi_transcripts.bed html
addlegend html
chromOffsets html
convertstrandinfo html
labelgenome html
labelplot html
maptocolors html
maptolwd html
opaque html
plotBed html
plotBedgraph html
plotBedpe html
plotGenes html
finding level-2 HTML links ... done
plotHic html
plotManhattan html
sortChrom html
zoombox html
zoomsregion html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'Sushi' is deprecated and will be removed from Bioconductor
version 3.16
** testing if installed package can be loaded from final location
Warning: Package 'Sushi' is deprecated and will be removed from Bioconductor
version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (Sushi)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TDARACNE' is missing or broken
done
Sushi.Rcheck/Sushi-Ex.timings
| name | user | system | elapsed | |
| SushiColors | 0.01 | 0.00 | 0.02 | |
| addlegend | 0.27 | 0.00 | 0.26 | |
| labelgenome | 0.77 | 0.13 | 0.91 | |
| labelplot | 0.01 | 0.01 | 0.03 | |
| maptocolors | 0.02 | 0.00 | 0.01 | |
| maptolwd | 0 | 0 | 0 | |
| opaque | 0 | 0 | 0 | |
| plotBed | 0.17 | 0.03 | 0.21 | |
| plotBedgraph | 0.00 | 0.02 | 0.01 | |
| plotBedpe | 0.14 | 0.00 | 0.14 | |
| plotGenes | 0.02 | 0.00 | 0.02 | |
| plotHic | 0.17 | 0.00 | 0.17 | |
| plotManhattan | 0.46 | 0.04 | 0.49 | |
| zoombox | 0.5 | 0.0 | 0.5 | |
| zoomsregion | 0.03 | 0.01 | 0.04 | |