Sushi 1.8.0
Douglas H Phanstiel
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Sushi | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf Sushi.buildbin-libdir Sushi.Rcheck && mkdir Sushi.buildbin-libdir Sushi.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Sushi.buildbin-libdir Sushi_1.8.0.tar.gz >Sushi.Rcheck\00install.out 2>&1 && cp Sushi.Rcheck\00install.out Sushi-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Sushi.buildbin-libdir --install="check:Sushi-install.out" --force-multiarch --no-vignettes --timings Sushi_1.8.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/Sushi.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.8.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [10s] 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
'D:/biocbld/bbs-3.2-bioc/meat/Sushi.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Sushi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'Sushi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Sushi' as Sushi_1.8.0.zip
* DONE (Sushi)