Douglas H Phanstiel
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Sushi |
| Branch: RELEASE_3_9 |
| Last Commit: d251181 |
| Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:29:50 -0400 (Wed, 16 Oct 2019).
| Package 1612/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Sushi 1.22.0 Douglas H Phanstiel
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Sushi |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sushi.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Sushi_1.22.0.tar.gz |
| StartedAt: 2019-10-16 07:26:58 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:29:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 149.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Sushi.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sushi.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Sushi_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Sushi.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.22.0'
* 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 ... OK
* 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
* 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 ... 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 ...
** 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 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/Sushi.Rcheck/00check.log'
for details.
Sushi.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Sushi_1.22.0.tar.gz && rm -rf Sushi.buildbin-libdir && mkdir Sushi.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Sushi.buildbin-libdir Sushi_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Sushi_1.22.0.zip && rm Sushi_1.22.0.tar.gz Sushi_1.22.0.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 4024k 100 4024k 0 0 40.0M 0 --:--:-- --:--:-- --:--:-- 42.7M
install for i386
* 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
** 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 'Sushi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Sushi' as Sushi_1.22.0.zip
* DONE (Sushi)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Sushi' successfully unpacked and MD5 sums checked
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Sushi.Rcheck/examples_i386/Sushi-Ex.timings
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Sushi.Rcheck/examples_x64/Sushi-Ex.timings
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