genoset 1.32.0
Peter M. Haverty
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/genoset | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/genoset.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genoset’ 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
* 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
.Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
.Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
.Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
.Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
.Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'GenoSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘prove.R’
Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...15c15
< IQR, mad, sd, var, xtabs
---
> IQR, mad, xtabs
20,32c20,24
< as.data.frame, cbind, colMeans, colSums, colnames, do.call,
< duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
< lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
< pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
< setdiff, sort, table, tapply, union, unique, unsplit, which,
< which.max, which.min
<
<
< Attaching package: 'S4Vectors'
<
< The following object is masked from 'package:base':
<
< expand.grid
---
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
> mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
> rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist, unsplit
41,57c33,37
< Attaching package: 'matrixStats'
<
< The following objects are masked from 'package:Biobase':
<
< anyMissing, rowMedians
<
<
< Attaching package: 'DelayedArray'
<
< The following objects are masked from 'package:matrixStats':
<
< colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
<
< The following object is masked from 'package:base':
<
< apply
<
---
> *** Genoset API Changes ***
> The genoset class is transitioning to extending
> RangedSummarizedExperiment rather than eSet. For this release,
> please use the RSE API as the eSet API has been deprecated
> (e.g. colnames instead of sampleNames). ***
77c57
< RUNIT TEST PROTOCOL -- Tue Aug 15 23:27:09 2017
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015
79c59
< Number of test functions: 32
---
> Number of test functions: 36
85,86c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36
88a69
> There were 19 warnings (use warnings() to see them)
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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/genoset.Rcheck/00check.log’
for details.